| ofs | hex dump | ascii |
|---|---|---|
| 0000 | 62 30 56 49 4d 20 37 2e 33 00 00 00 00 10 00 00 68 d1 28 52 d2 0a 60 01 a2 31 00 00 63 61 6c 76 | b0VIM.7.3.......h.(R..`..1..calv |
| 0020 | 69 6e 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | in.............................. |
| 0040 | 00 00 00 00 62 61 72 6e 61 62 61 73 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ....barnabas.................... |
| 0060 | 00 00 00 00 00 00 00 00 00 00 00 00 7e 63 61 6c 76 69 6e 2f 73 72 63 2f 71 75 69 6b 72 2f 64 6f | ............~calvin/src/quikr/do |
| 0080 | 63 2f 63 6c 69 2e 6d 61 72 6b 64 6f 77 6e 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | c/cli.markdown.................. |
| 00a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 00c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 00e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0100 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0120 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0140 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0160 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0180 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 01a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 01c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 01e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0200 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0220 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0240 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0260 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0280 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 02a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 02c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 02e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0300 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0320 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0340 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0360 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0380 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 03a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 03c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 03e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0d 00 33 32 31 30 00 00 00 00 23 22 21 20 13 12 55 00 | ................3210....#"!...U. |
| 0400 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0420 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0440 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0460 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0480 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 04a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 04c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 04e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0500 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0520 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0540 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0560 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0580 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 05a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 05c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 05e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0600 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0620 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0640 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0660 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0680 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 06a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 06c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 06e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0700 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0720 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0740 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0760 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0780 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 07a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 07c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 07e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0800 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0820 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0840 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0860 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0880 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 08a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 08c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 08e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0900 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0920 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0940 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0960 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0980 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 09a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 09c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 09e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0a00 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0a20 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0a40 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0a60 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0a80 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0aa0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ac0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ae0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0b00 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0b20 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0b40 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0b60 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0b80 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ba0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0bc0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0be0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0c00 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0c20 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0c40 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0c60 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0c80 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ca0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0cc0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ce0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0d00 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0d20 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0d40 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0d60 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0d80 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0da0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0dc0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0de0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0e00 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0e20 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0e40 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0e60 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0e80 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ea0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ec0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0ee0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0f00 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0f20 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0f40 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0f60 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0f80 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0fa0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0fc0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 0fe0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1000 | 74 70 02 00 7f 00 00 00 02 00 00 00 00 00 00 00 4d 00 00 00 00 00 00 00 01 00 00 00 00 00 00 00 | tp..............M............... |
| 1020 | 01 00 00 00 00 00 00 00 03 00 00 00 00 00 00 00 27 00 00 00 00 00 00 00 4e 00 00 00 00 00 00 00 | ................'.......N....... |
| 1040 | 01 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1060 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1080 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 10a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 10c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 10e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1100 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1120 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1140 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1160 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1180 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 11a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 11c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 11e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1200 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1220 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1240 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1260 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1280 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 12a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 12c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 12e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1300 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1320 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1340 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1360 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1380 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 13a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 13c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 13e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1400 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1420 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1440 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1460 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1480 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 14a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 14c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 14e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1500 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1520 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1540 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1560 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1580 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 15a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 15c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 15e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1600 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1620 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1640 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1660 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1680 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 16a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 16c0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 16e0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1700 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1720 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1740 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1760 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 1780 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 17a0 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
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| 2000 | 61 64 00 00 41 00 00 00 91 01 00 00 00 10 00 00 4d 00 00 00 00 00 00 00 df 0f 00 00 91 0f 00 00 | ad..A...........M............... |
| 2020 | 40 0f 00 00 f0 0e 00 00 ae 0e 00 00 ad 0e 00 00 67 0e 00 00 4e 0e 00 00 4d 0e 00 00 3a 0e 00 00 | @...............g...N...M...:... |
| 2040 | ee 0d 00 00 a3 0d 00 00 a2 0d 00 00 94 0d 00 00 47 0d 00 00 3d 0d 00 00 3c 0d 00 00 1f 0d 00 00 | ................G...=...<....... |
| 2060 | e3 0c 00 00 b0 0c 00 00 67 0c 00 00 44 0c 00 00 20 0c 00 00 1f 0c 00 00 0f 0c 00 00 be 0b 00 00 | ........g...D................... |
| 2080 | 70 0b 00 00 23 0b 00 00 d6 0a 00 00 ae 0a 00 00 ad 0a 00 00 5e 0a 00 00 5d 0a 00 00 51 0a 00 00 | p...#...............^...]...Q... |
| 20a0 | 07 0a 00 00 c0 09 00 00 bf 09 00 00 b1 09 00 00 80 09 00 00 7f 09 00 00 68 09 00 00 24 09 00 00 | ........................h...$... |
| 20c0 | b7 08 00 00 63 08 00 00 1d 08 00 00 de 07 00 00 5b 07 00 00 3b 07 00 00 1a 07 00 00 19 07 00 00 | ....c...........[...;........... |
| 20e0 | ff 06 00 00 b1 06 00 00 61 06 00 00 26 06 00 00 25 06 00 00 d6 05 00 00 8a 05 00 00 3a 05 00 00 | ........a...&...%...........:... |
| 2100 | 39 05 00 00 0a 05 00 00 09 05 00 00 b9 04 00 00 6a 04 00 00 1f 04 00 00 12 04 00 00 c1 03 00 00 | 9...............j............... |
| 2120 | 9e 03 00 00 9d 03 00 00 8d 03 00 00 8c 03 00 00 69 03 00 00 19 03 00 00 d7 02 00 00 6a 02 00 00 | ................i...........j... |
| 2140 | 16 02 00 00 d0 01 00 00 91 01 00 00 90 01 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 2160 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 | ................................ |
| 2180 | 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 20 20 20 20 2d 6c 2c 20 2d 2d 6c 61 6d 62 64 | .....................-l,.--lambd |
| 21a0 | 61 20 6c 61 6d 62 64 61 20 76 61 6c 75 65 20 74 6f 20 75 73 65 2e 20 28 64 65 66 61 75 6c 74 20 | a.lambda.value.to.use..(default. |
| 21c0 | 76 61 6c 75 65 20 69 73 20 31 30 30 30 30 29 00 20 20 20 20 2d 6b 2c 20 2d 2d 6b 6d 65 72 20 73 | value.is.10000).....-k,.--kmer.s |
| 21e0 | 70 65 63 69 66 79 20 77 68 61 74 20 73 69 7a 65 20 6f 66 20 6b 6d 65 72 20 74 6f 20 75 73 65 2e | pecify.what.size.of.kmer.to.use. |
| 2200 | 20 28 64 65 66 61 75 6c 74 20 76 61 6c 75 65 20 69 73 20 36 29 00 20 20 20 20 2d 73 2c 20 2d 2d | .(default.value.is.6).....-s,.-- |
| 2220 | 73 65 6e 73 69 6e 67 2d 6d 61 74 72 69 78 20 6c 6f 63 61 74 69 6f 6e 20 6f 66 20 74 68 65 20 73 | sensing-matrix.location.of.the.s |
| 2240 | 65 6e 73 69 6e 67 20 6d 61 74 72 69 78 2e 20 28 73 65 6e 73 69 6e 67 20 66 72 6f 6d 20 71 75 69 | ensing.matrix..(sensing.from.qui |
| 2260 | 6b 72 5f 74 72 61 69 6e 29 00 20 20 20 20 2d 66 2c 20 2d 2d 73 65 6e 73 69 6e 67 2d 66 61 73 74 | kr_train).....-f,.--sensing-fast |
| 2280 | 61 20 6c 6f 63 61 74 69 6f 6e 20 6f 66 20 74 68 65 20 66 61 73 74 61 20 66 69 6c 65 20 64 61 74 | a.location.of.the.fasta.file.dat |
| 22a0 | 61 62 61 73 65 20 75 73 65 64 20 74 6f 20 63 72 65 61 74 65 20 74 68 65 20 73 65 6e 73 69 6e 67 | abase.used.to.create.the.sensing |
| 22c0 | 20 6d 61 74 72 69 78 20 28 66 61 73 74 61 20 66 6f 72 6d 61 74 29 00 20 20 20 20 72 65 61 64 73 | .matrix.(fasta.format).....reads |
| 22e0 | 20 28 6e 6f 74 65 20 65 61 63 68 20 66 69 6c 65 20 73 68 6f 75 6c 64 20 63 6f 72 72 65 73 70 6f | .(note.each.file.should.correspo |
| 2300 | 6e 64 20 74 6f 20 61 20 73 65 70 61 72 61 74 65 20 73 61 6d 70 6c 65 29 00 20 20 20 20 2d 69 2c | nd.to.a.separate.sample).....-i, |
| 2320 | 20 2d 2d 69 6e 70 75 74 2d 64 69 72 65 63 74 6f 72 79 20 74 68 65 20 64 69 72 65 63 74 6f 72 79 | .--input-directory.the.directory |
| 2340 | 20 63 6f 6e 74 61 69 6e 69 6e 67 20 74 68 65 20 73 61 6d 70 6c 65 73 27 20 66 61 73 74 61 20 66 | .containing.the.samples'.fasta.f |
| 2360 | 69 6c 65 73 20 6f 66 20 00 20 20 20 20 6d 75 6c 74 69 66 61 73 74 61 5f 74 6f 5f 6f 74 75 27 73 | iles.of......multifasta_to_otu's |
| 2380 | 20 61 72 67 75 6d 65 6e 74 73 3a 00 00 23 23 23 23 20 55 73 61 67 65 20 23 23 23 23 00 00 20 20 | .arguments:..####.Usage.####.... |
| 23a0 | 2e 66 61 20 61 72 65 20 76 61 6c 69 64 20 77 68 69 6c 65 20 2e 66 6e 61 20 69 73 20 4e 4f 54 29 | .fa.are.valid.while..fna.is.NOT) |
| 23c0 | 00 2a 20 46 61 73 74 61 20 66 69 6c 65 73 20 6f 66 20 72 65 61 64 73 20 6d 75 73 74 20 68 61 76 | .*.Fasta.files.of.reads.must.hav |
| 23e0 | 65 20 61 20 73 75 66 66 69 78 20 74 68 61 74 20 73 74 61 72 74 73 20 77 69 74 68 20 2e 66 61 20 | e.a.suffix.that.starts.with..fa. |
| 2400 | 28 65 2e 67 2e 3a 20 2e 66 61 73 74 61 20 61 6e 64 00 20 20 64 69 72 65 63 74 6f 72 79 29 00 20 | (e.g.:..fasta.and...directory).. |
| 2420 | 20 68 69 64 64 65 6e 20 66 69 6c 65 73 20 74 68 61 74 20 74 68 65 20 6f 70 65 72 61 74 69 6e 67 | .hidden.files.that.the.operating |
| 2440 | 20 73 79 73 74 65 6d 20 6d 61 79 20 67 65 6e 65 72 61 74 65 2c 20 61 72 65 20 61 6c 6c 6f 77 65 | .system.may.generate,.are.allowe |
| 2460 | 64 20 69 6e 20 74 68 61 74 00 20 20 69 6e 74 6f 20 6f 6e 65 20 64 69 72 65 63 74 6f 72 79 20 77 | d.in.that...into.one.directory.w |
| 2480 | 69 74 68 6f 75 74 20 61 6e 79 20 6f 74 68 65 72 20 66 69 6c 65 20 69 6e 20 74 68 61 74 20 64 69 | ithout.any.other.file.in.that.di |
| 24a0 | 72 65 63 74 6f 72 79 20 28 66 6f 72 20 65 78 61 6d 70 6c 65 2c 20 6e 6f 00 2a 20 50 6c 65 61 73 | rectory.(for.example,.no.*.Pleas |
| 24c0 | 65 20 6e 61 6d 65 20 66 61 73 74 61 20 66 69 6c 65 73 20 6f 66 20 73 61 6d 70 6c 65 20 72 65 61 | e.name.fasta.files.of.sample.rea |
| 24e0 | 64 73 20 77 69 74 68 20 3c 73 61 6d 70 6c 65 20 69 64 3e 2e 66 61 3c 2a 3e 20 61 6e 64 20 70 6c | ds.with.<sample.id>.fa<*>.and.pl |
| 2500 | 61 63 65 20 74 68 65 6d 00 00 23 23 23 20 50 72 65 2d 70 72 6f 63 65 73 73 69 6e 67 20 6f 66 20 | ace.them..###.Pre-processing.of. |
| 2520 | 4d 75 6c 74 69 66 61 73 74 61 5c 5f 74 6f 5c 5f 6f 74 75 20 20 23 23 23 00 00 77 69 74 68 20 61 | Multifasta\_to\_otu..###..with.a |
| 2540 | 73 70 65 63 69 66 69 65 64 20 6e 75 6d 62 65 72 20 6f 66 20 6a 6f 62 73 2e 20 4f 74 68 65 72 77 | specified.number.of.jobs..Otherw |
| 2560 | 69 73 65 20 70 79 74 68 6f 6e 20 77 69 74 68 20 72 75 6e 20 6f 6e 65 20 6a 6f 62 20 70 65 72 20 | ise.python.with.run.one.job.per. |
| 2580 | 63 70 75 20 63 6f 72 65 2e 00 72 65 64 75 63 65 20 74 68 65 20 6e 75 6d 62 65 72 20 6f 66 20 63 | cpu.core..reduce.the.number.of.c |
| 25a0 | 6f 72 65 73 20 75 73 65 64 2c 20 61 6e 64 20 74 68 75 73 20 6d 65 6d 6f 72 79 2c 20 62 79 20 73 | ores.used,.and.thus.memory,.by.s |
| 25c0 | 70 65 63 69 66 79 69 6e 67 20 74 68 65 20 2d 6a 20 66 6c 61 67 00 57 61 72 6e 69 6e 67 3a 20 74 | pecifying.the.-j.flag.Warning:.t |
| 25e0 | 68 69 73 20 70 72 6f 67 72 61 6d 20 77 69 6c 6c 20 75 73 65 20 61 20 6c 61 72 67 65 20 61 6d 6f | his.program.will.use.a.large.amo |
| 2600 | 75 6e 74 20 6f 66 20 6d 65 6d 6f 72 79 2c 20 61 6e 64 20 43 50 55 20 74 69 6d 65 2e 20 59 6f 75 | unt.of.memory,.and.CPU.time..You |
| 2620 | 20 63 61 6e 00 00 6e 75 6d 62 65 72 20 6f 66 20 74 69 6d 65 73 20 61 20 73 70 65 63 69 6d 65 6e | .can..number.of.times.a.specimen |
| 2640 | 20 77 61 73 20 73 65 65 6e 20 69 6e 20 61 6c 6c 20 6f 66 20 74 68 65 20 73 61 6d 70 6c 65 73 20 | .was.seen.in.all.of.the.samples. |
| 2660 | 00 74 6f 20 69 6e 70 75 74 20 61 73 20 6d 61 6e 79 20 66 61 73 74 61 20 66 69 6c 65 73 20 61 73 | .to.input.as.many.fasta.files.as |
| 2680 | 20 74 68 65 79 20 6c 69 6b 65 2c 20 61 6e 64 20 74 68 65 6e 20 72 65 74 75 72 6e 73 20 61 6e 20 | .they.like,.and.then.returns.an. |
| 26a0 | 4f 54 55 20 74 61 62 6c 65 20 6f 66 20 74 68 65 00 54 68 65 20 4d 75 6c 74 69 66 61 73 74 61 5c | OTU.table.of.the.The.Multifasta\ |
| 26c0 | 5f 74 6f 5c 5f 6f 74 75 20 74 6f 6f 6c 20 69 73 20 61 20 68 61 6e 64 79 20 77 72 61 70 70 65 72 | _to\_otu.tool.is.a.handy.wrapper |
| 26e0 | 20 66 6f 72 20 71 75 69 6b 72 20 77 68 69 63 68 20 6c 65 74 73 20 74 68 65 20 75 73 65 72 00 23 | .for.quikr.which.lets.the.user.# |
| 2700 | 23 20 4d 75 6c 74 69 66 61 73 74 61 5c 5f 74 6f 5c 5f 6f 74 75 20 23 23 00 00 20 20 20 20 2d 56 | #.Multifasta\_to\_otu.##......-V |
| 2720 | 2c 20 2d 2d 76 65 72 73 69 6f 6e 20 70 72 69 6e 74 20 76 65 72 73 69 6f 6e 2e 00 20 20 20 20 2d | ,.--version.print.version......- |
| 2740 | 76 2c 20 2d 2d 76 65 72 62 6f 73 65 20 76 65 72 62 6f 73 65 20 6d 6f 64 65 2e 00 20 20 20 20 2d | v,.--verbose.verbose.mode......- |
| 2760 | 6f 2c 20 2d 2d 6f 75 74 70 75 74 20 4f 54 55 5f 46 52 41 43 54 49 4f 4e 5f 50 52 45 53 45 4e 54 | o,.--output.OTU_FRACTION_PRESENT |
| 2780 | 20 61 20 76 65 63 74 6f 72 20 72 65 70 72 65 73 65 6e 74 69 6e 67 20 74 68 65 20 70 65 72 63 65 | .a.vector.representing.the.perce |
| 27a0 | 6e 74 61 67 65 20 6f 66 20 64 61 74 61 62 61 73 65 20 73 65 71 75 65 6e 63 65 27 73 20 70 72 65 | ntage.of.database.sequence's.pre |
| 27c0 | 73 65 6e 63 65 20 69 6e 20 73 61 6d 70 6c 65 2e 20 28 63 73 76 20 6f 75 74 70 75 74 29 00 20 20 | sence.in.sample..(csv.output)... |
| 27e0 | 20 20 2d 6c 2c 20 2d 2d 6c 61 6d 62 64 61 20 6c 61 6d 62 64 61 20 76 61 6c 75 65 20 74 6f 20 75 | ..-l,.--lambda.lambda.value.to.u |
| 2800 | 73 65 2e 20 28 64 65 66 61 75 6c 74 20 76 61 6c 75 65 20 69 73 20 31 30 30 30 30 29 00 20 20 20 | se..(default.value.is.10000).... |
| 2820 | 20 2d 6b 2c 20 2d 2d 6b 6d 65 72 20 73 70 65 63 69 66 79 20 77 68 61 74 20 73 69 7a 65 20 6f 66 | .-k,.--kmer.specify.what.size.of |
| 2840 | 20 6b 6d 65 72 20 74 6f 20 75 73 65 2e 20 28 64 65 66 61 75 6c 74 20 76 61 6c 75 65 20 69 73 20 | .kmer.to.use..(default.value.is. |
| 2860 | 36 29 00 20 20 20 20 2d 73 2c 20 2d 2d 73 65 6e 73 69 6e 67 2d 6d 61 74 72 69 78 20 6c 6f 63 61 | 6).....-s,.--sensing-matrix.loca |
| 2880 | 74 69 6f 6e 20 6f 66 20 74 68 65 20 73 65 6e 73 69 6e 67 20 6d 61 74 72 69 78 2e 20 28 74 72 61 | tion.of.the.sensing.matrix..(tra |
| 28a0 | 69 6e 65 64 20 66 72 6f 6d 20 71 75 69 6b 72 5f 74 72 61 69 6e 29 00 20 20 20 20 2d 66 2c 20 2d | ined.from.quikr_train).....-f,.- |
| 28c0 | 2d 73 65 6e 73 69 6e 67 2d 66 61 73 74 61 20 6c 6f 63 61 74 69 6f 6e 20 6f 66 20 74 68 65 20 66 | -sensing-fasta.location.of.the.f |
| 28e0 | 61 73 74 61 20 66 69 6c 65 20 64 61 74 61 62 61 73 65 20 75 73 65 64 20 74 6f 20 63 72 65 61 74 | asta.file.database.used.to.creat |
| 2900 | 65 20 74 68 65 20 73 65 6e 73 69 6e 67 20 6d 61 74 72 69 78 20 28 66 61 73 74 61 20 66 6f 72 6d | e.the.sensing.matrix.(fasta.form |
| 2920 | 61 74 29 00 20 20 20 20 2d 69 2c 20 2d 2d 69 6e 70 75 74 20 74 68 65 20 73 61 6d 70 6c 65 27 73 | at).....-i,.--input.the.sample's |
| 2940 | 20 66 61 73 74 61 20 66 69 6c 65 20 6f 66 20 4e 47 53 20 52 45 41 44 53 20 28 66 61 73 74 61 20 | .fasta.file.of.NGS.READS.(fasta. |
| 2960 | 66 6f 72 6d 61 74 29 00 20 20 20 20 71 75 69 6b 72 27 73 20 61 72 67 75 6d 65 6e 74 73 3a 00 00 | format).....quikr's.arguments:.. |
| 2980 | 71 75 69 6b 72 20 72 65 74 75 72 6e 73 20 74 68 65 20 73 6f 6c 75 74 69 6f 6e 20 76 65 63 74 6f | quikr.returns.the.solution.vecto |
| 29a0 | 72 20 61 73 20 61 20 63 73 76 20 66 69 6c 65 2e 00 23 23 23 20 55 73 61 67 65 20 23 23 23 00 00 | r.as.a.csv.file..###.Usage.###.. |
| 29c0 | 69 6e 70 75 74 20 46 41 53 54 41 20 66 69 6c 65 2e 20 59 6f 75 20 6e 65 65 64 20 74 6f 20 74 72 | input.FASTA.file..You.need.to.tr |
| 29e0 | 61 69 6e 20 61 20 6d 61 74 72 69 78 20 6f 72 20 64 6f 77 6e 6c 6f 61 64 20 61 20 6e 65 77 20 6d | ain.a.matrix.or.download.a.new.m |
| 2a00 | 61 74 72 69 78 20 00 51 75 69 6b 72 20 72 65 74 75 72 6e 73 20 74 68 65 20 65 73 74 69 6d 61 74 | atrix..Quikr.returns.the.estimat |
| 2a20 | 65 64 20 66 72 65 71 75 65 6e 63 69 65 73 20 6f 66 20 62 61 74 63 74 65 72 69 61 20 70 72 65 73 | ed.frequencies.of.batcteria.pres |
| 2a40 | 65 6e 74 20 77 68 65 6e 20 67 69 76 65 6e 20 61 00 23 23 20 51 75 69 6b 72 20 23 23 00 00 20 20 | ent.when.given.a.##.Quikr.##.... |
| 2a60 | 20 20 71 75 69 6b 72 5f 74 72 61 69 6e 20 2d 69 20 67 67 39 34 5f 64 61 74 61 62 61 73 65 2e 66 | ..quikr_train.-i.gg94_database.f |
| 2a80 | 61 73 74 61 20 2d 6f 20 67 67 39 34 5f 73 65 6e 73 69 6e 67 5f 64 61 74 61 62 61 73 65 2e 6d 61 | asta.-o.gg94_sensing_database.ma |
| 2aa0 | 74 72 69 78 2e 67 7a 20 2d 6b 20 36 00 00 6d 61 74 72 69 78 20 61 73 20 67 67 39 34 5c 5f 73 65 | trix.gz.-k.6..matrix.as.gg94\_se |
| 2ac0 | 6e 73 69 6e 67 5c 5f 64 61 74 61 62 73 65 2e 6e 70 79 2e 67 7a 00 67 7a 69 70 2e 20 49 74 20 74 | nsing\_databse.npy.gz.gzip..It.t |
| 2ae0 | 61 6b 65 73 20 74 68 65 20 67 67 39 34 5c 5f 64 61 74 61 62 61 73 65 2e 66 61 73 74 61 20 61 73 | akes.the.gg94\_database.fasta.as |
| 2b00 | 20 61 6e 20 69 6e 70 75 74 20 61 6e 64 20 6f 75 74 70 75 74 73 20 74 68 65 20 73 65 6e 73 69 6e | .an.input.and.outputs.the.sensin |
| 2b20 | 67 20 00 74 68 65 20 64 61 74 61 62 61 73 65 2c 20 74 68 65 20 6d 61 74 72 69 78 20 65 61 73 69 | g..the.database,.the.matrix.easi |
| 2b40 | 6c 79 20 61 63 68 69 65 76 65 73 20 61 20 68 69 67 68 20 63 6f 6d 70 72 65 73 73 69 6f 6e 20 72 | ly.achieves.a.high.compression.r |
| 2b60 | 61 74 69 6f 2c 20 65 76 65 6e 20 77 69 74 68 00 74 68 65 20 6f 75 74 70 75 74 20 6d 61 74 72 69 | atio,.even.with.the.output.matri |
| 2b80 | 78 20 73 69 6e 63 65 20 69 74 20 63 61 6e 20 62 65 20 76 65 72 79 20 6c 61 72 67 65 2e 20 42 65 | x.since.it.can.be.very.large..Be |
| 2ba0 | 63 61 75 73 65 20 6f 66 20 74 68 65 20 73 70 61 72 73 65 20 6e 61 74 75 72 65 20 6f 66 00 48 65 | cause.of.the.sparse.nature.of.He |
| 2bc0 | 72 65 20 69 73 20 61 6e 20 65 78 61 6d 70 6c 65 20 6f 6e 20 68 6f 77 20 74 6f 20 74 72 61 69 6e | re.is.an.example.on.how.to.train |
| 2be0 | 20 61 20 64 61 74 61 62 61 73 65 2e 20 54 68 69 73 20 75 73 65 73 20 74 68 65 20 2d 7a 20 66 6c | .a.database..This.uses.the.-z.fl |
| 2c00 | 61 67 20 74 6f 20 63 6f 6d 70 72 65 73 73 00 23 23 23 20 45 78 61 6d 70 6c 65 20 23 23 23 00 00 | ag.to.compress.###.Example.###.. |
| 2c20 | 20 20 20 20 20 20 2d 56 2c 20 2d 2d 76 65 72 73 69 6f 6e 2c 20 70 72 69 6e 74 20 76 65 72 73 69 | ......-V,.--version,.print.versi |
| 2c40 | 6f 6e 2e 00 20 20 20 20 20 20 2d 76 2c 20 2d 2d 76 65 72 62 6f 73 65 2c 20 76 65 72 62 6f 73 65 | on........-v,.--verbose,.verbose |
| 2c60 | 20 6d 6f 64 65 2e 00 20 20 20 20 20 20 2d 6b 2c 20 2d 2d 6b 6d 65 72 2c 20 73 70 65 63 69 66 69 | .mode........-k,.--kmer,.specifi |
| 2c80 | 79 20 77 68 61 20 73 69 7a 65 20 6f 66 20 6b 6d 65 72 20 74 6f 20 75 73 65 2e 20 28 64 65 66 61 | y.wha.size.of.kmer.to.use..(defa |
| 2ca0 | 75 6c 74 20 76 61 6c 75 65 20 69 73 20 36 29 00 20 20 20 20 20 20 2d 6f 2c 20 2d 2d 6f 75 74 70 | ult.value.is.6).......-o,.--outp |
| 2cc0 | 75 74 2c 20 74 68 65 20 73 65 6e 73 69 6e 67 20 6d 61 74 72 69 78 20 28 74 65 78 74 20 66 69 6c | ut,.the.sensing.matrix.(text.fil |
| 2ce0 | 65 29 00 20 20 20 20 20 20 2d 69 2c 20 2d 2d 69 6e 70 75 74 2c 20 74 68 65 20 64 61 74 61 62 61 | e).......-i,.--input,.the.databa |
| 2d00 | 73 65 20 6f 66 20 73 65 71 75 65 6e 63 65 73 20 28 66 61 73 74 61 20 66 6f 72 6d 61 74 29 00 20 | se.of.sequences.(fasta.format).. |
| 2d20 | 20 20 20 71 75 69 6b 72 5f 74 72 61 69 6e 27 73 20 61 72 67 75 6d 65 6e 74 73 3a 00 00 66 75 6e | ...quikr_train's.arguments:..fun |
| 2d40 | 63 74 69 6f 6e 2e 00 71 75 69 6b 72 5c 5f 74 72 61 69 6e 20 72 65 74 75 72 6e 73 20 61 20 63 75 | ction..quikr\_train.returns.a.cu |
| 2d60 | 73 74 6f 6d 20 73 65 6e 73 69 6e 67 20 6d 61 74 72 69 78 20 74 68 61 74 20 63 61 6e 20 62 65 20 | stom.sensing.matrix.that.can.be. |
| 2d80 | 75 73 65 64 20 77 69 74 68 20 74 68 65 20 71 75 69 6b 72 00 23 23 23 20 55 73 61 67 65 20 23 23 | used.with.the.quikr.###.Usage.## |
| 2da0 | 23 00 00 42 65 66 6f 72 65 20 72 75 6e 6e 69 6e 67 20 74 68 65 20 71 75 69 6b 72 20 75 74 69 6c | #..Before.running.the.quikr.util |
| 2dc0 | 69 74 79 2c 20 79 6f 75 20 6e 65 65 64 20 74 6f 20 67 65 6e 65 72 61 74 65 20 74 68 65 20 73 65 | ity,.you.need.to.generate.the.se |
| 2de0 | 6e 73 69 6e 67 20 6d 61 74 72 69 78 2e 00 54 68 65 20 71 75 69 6b 72 5c 5f 74 72 61 69 6e 20 69 | nsing.matrix..The.quikr\_train.i |
| 2e00 | 73 20 61 20 74 6f 6f 6c 20 74 6f 20 74 72 61 69 6e 20 61 20 64 61 74 61 62 61 73 65 20 66 6f 72 | s.a.tool.to.train.a.database.for |
| 2e20 | 20 75 73 65 20 77 69 74 68 20 74 68 65 20 71 75 69 6b 72 20 74 6f 6f 6c 2e 00 23 23 20 51 75 69 | .use.with.the.quikr.tool..##.Qui |
| 2e40 | 6b 72 5c 5f 74 72 61 69 6e 20 23 23 00 00 72 65 73 70 65 63 74 69 76 65 20 6d 61 6e 75 61 6c 20 | kr\_train.##..respective.manual. |
| 2e60 | 70 61 67 65 73 2e 00 46 6f 72 20 6d 6f 72 65 20 69 6e 2d 64 65 70 74 68 20 69 6e 66 6f 72 6d 61 | pages..For.more.in-depth.informa |
| 2e80 | 74 69 6f 6e 20 61 62 6f 75 74 20 74 68 65 73 65 20 74 6f 6f 6c 73 20 70 6c 65 61 73 65 20 72 65 | tion.about.these.tools.please.re |
| 2ea0 | 66 65 72 20 74 6f 20 74 68 65 69 72 00 00 75 74 69 6c 69 74 69 65 73 20 61 72 65 20 77 72 69 74 | fer.to.their..utilities.are.writ |
| 2ec0 | 74 65 6e 20 69 6e 20 43 20 61 6e 64 20 75 74 69 6c 69 7a 65 20 4f 70 65 6e 4d 50 20 66 6f 72 20 | ten.in.C.and.utilize.OpenMP.for. |
| 2ee0 | 6d 75 6c 74 69 74 68 72 65 61 64 69 6e 67 2e 00 61 6e 64 20 6a 6f 62 20 6d 61 6e 61 67 65 6d 65 | multithreading..and.job.manageme |
| 2f00 | 6e 74 2c 20 61 73 20 77 65 6c 6c 20 61 73 20 66 61 73 74 65 72 20 70 72 6f 63 65 73 73 69 6e 67 | nt,.as.well.as.faster.processing |
| 2f20 | 20 61 6e 64 20 6c 6f 77 65 72 20 6d 65 6d 6f 72 79 20 75 73 61 67 65 2e 20 54 68 65 73 65 20 00 | .and.lower.memory.usage..These.. |
| 2f40 | 6d 6f 64 75 6c 65 20 61 6e 64 20 74 68 65 20 6d 61 74 6c 61 62 20 69 6d 70 6c 65 6d 65 6e 74 61 | module.and.the.matlab.implementa |
| 2f60 | 74 69 6f 6e 2e 20 54 68 65 20 61 64 76 61 6e 74 61 67 65 20 6f 66 20 74 68 69 73 20 69 73 20 65 | tion..The.advantage.of.this.is.e |
| 2f80 | 61 73 65 20 6f 66 20 73 63 72 69 70 74 69 6e 67 00 51 75 69 6b 72 20 68 61 73 20 74 68 72 65 65 | ase.of.scripting.Quikr.has.three |
| 2fa0 | 20 63 6f 6d 6d 61 6e 64 2d 6c 69 6e 65 20 75 74 69 6c 69 74 69 65 73 20 74 68 61 74 20 6d 69 72 | .command-line.utilities.that.mir |
| 2fc0 | 72 6f 72 20 74 68 65 20 62 65 68 61 76 69 6f 72 20 6f 66 20 74 68 65 20 70 79 74 68 6f 6e 00 23 | ror.the.behavior.of.the.python.# |
| 2fe0 | 20 51 75 69 6b 72 20 43 6f 6d 6d 61 6e 64 20 4c 69 6e 65 20 55 74 69 6c 69 74 69 65 73 20 23 00 | .Quikr.Command.Line.Utilities.#. |
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| 3020 | 03 0f 00 00 e3 0e 00 00 c1 0e 00 00 c0 0e 00 00 90 0e 00 00 8f 0e 00 00 42 0e 00 00 21 0e 00 00 | ........................B...!... |
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| 3060 | e0 0c 00 00 bb 0c 00 00 7f 0c 00 00 7e 0c 00 00 6a 0c 00 00 69 0c 00 00 0a 0c 00 00 91 0b 00 00 | ............~...j...i........... |
| 3080 | 1e 0b 00 00 ac 0a 00 00 ab 0a 00 00 aa 0a 00 00 91 0a 00 00 47 0a 00 00 21 0a 00 00 20 0a 00 00 | ....................G...!....... |
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| 3920 | 50 41 54 48 20 3d 20 24 50 41 54 48 3a 2f 70 61 74 68 2f 74 6f 2f 71 75 69 6b 72 2f 73 72 63 2f | PATH.=.$PATH:/path/to/quikr/src/ |
| 3940 | 6e 62 63 2f 00 20 20 20 20 6d 76 20 2f 70 61 74 68 2f 74 6f 2f 71 75 69 6b 72 2f 73 72 63 2f 6e | nbc/.....mv./path/to/quikr/src/n |
| 3960 | 62 63 2f 63 6f 75 6e 74 20 2f 70 61 74 68 2f 74 6f 2f 71 75 69 6b 72 2f 73 72 63 2f 6e 62 63 2f | bc/count./path/to/quikr/src/nbc/ |
| 3980 | 63 6f 75 6e 74 2d 6b 6d 65 72 73 00 20 00 6c 6f 63 61 74 69 6f 6e 20 6f 66 20 74 68 65 73 65 20 | count-kmers...location.of.these. |
| 39a0 | 62 69 6e 61 72 69 65 73 20 69 6e 20 74 68 65 20 74 65 72 6d 69 6e 61 6c 20 62 65 66 6f 72 65 20 | binaries.in.the.terminal.before. |
| 39c0 | 72 75 6e 6e 69 6e 67 20 74 68 65 20 63 6f 6d 6d 61 6e 64 3a 00 49 66 20 79 6f 75 20 68 61 76 65 | running.the.command:.If.you.have |
| 39e0 | 20 6e 6f 74 20 69 6e 73 74 61 6c 6c 65 64 20 71 75 69 6b 72 20 73 79 73 74 65 6d 2d 77 69 64 65 | .not.installed.quikr.system-wide |
| 3a00 | 2c 20 79 6f 75 27 6c 6c 20 6e 65 65 64 20 74 6f 20 61 64 64 20 74 68 65 20 66 6f 6c 64 65 72 00 | ,.you'll.need.to.add.the.folder. |
| 3a20 | 00 24 50 41 54 48 2c 20 61 6e 64 20 74 68 61 74 20 74 68 65 79 20 61 72 65 20 65 78 65 63 75 74 | .$PATH,.and.that.they.are.execut |
| 3a40 | 61 62 6c 65 2e 20 00 4d 61 6b 65 20 73 75 72 65 20 74 68 61 74 20 79 6f 75 20 68 61 76 65 20 74 | able...Make.sure.that.you.have.t |
| 3a60 | 68 65 20 63 6f 75 6e 74 2d 6b 6d 65 72 73 20 61 6e 64 20 70 72 6f 62 61 62 6c 69 6c 74 69 65 73 | he.count-kmers.and.probablilties |
| 3a80 | 2d 62 79 2d 72 65 61 64 20 69 6e 20 79 6f 75 72 00 23 23 20 42 72 6f 6b 65 6e 20 50 69 70 65 20 | -by-read.in.your.##.Broken.Pipe. |
| 3aa0 | 45 72 72 6f 72 73 20 23 23 00 00 00 20 20 20 20 6d 61 6b 65 5f 33 64 5f 70 6c 6f 74 73 2e 70 79 | Errors.##.......make_3d_plots.py |
| 3ac0 | 20 2d 69 20 3c 71 75 69 6b 72 5f 6f 74 75 5f 70 72 6f 6a 65 63 74 5f 6e 61 6d 65 3e 5f 77 65 69 | .-i.<quikr_otu_project_name>_wei |
| 3ae0 | 67 68 74 65 64 2e 74 78 74 20 2d 6f 20 3c 33 64 5f 70 63 6f 61 5f 70 6c 6f 74 64 69 72 65 63 74 | ghted.txt.-o.<3d_pcoa_plotdirect |
| 3b00 | 6f 72 79 3e 20 2d 6d 20 3c 71 69 69 6d 65 5f 6d 65 74 61 64 61 74 61 5f 66 69 6c 65 3e 00 20 20 | ory>.-m.<qiime_metadata_file>... |
| 3b20 | 20 20 70 72 69 6e 63 69 70 61 6c 5f 63 6f 6f 72 64 69 6e 61 74 65 73 2e 70 79 20 2d 69 20 62 65 | ..principal_coordinates.py.-i.be |
| 3b40 | 74 61 5f 64 69 76 2f 77 65 69 67 68 74 65 64 5f 75 6e 69 66 72 61 63 5f 3c 71 75 69 6b 72 5f 6f | ta_div/weighted_unifrac_<quikr_o |
| 3b60 | 74 75 3e 2e 74 78 74 20 2d 6f 20 3c 71 75 69 6b 72 5f 6f 74 75 5f 70 72 6f 6a 65 63 74 5f 6e 61 | tu>.txt.-o.<quikr_otu_project_na |
| 3b80 | 6d 65 3e 5f 77 65 69 67 68 74 65 64 2e 74 78 74 00 20 20 20 20 62 65 74 61 5f 64 69 76 65 72 73 | me>_weighted.txt.....beta_divers |
| 3ba0 | 69 74 79 2e 70 79 20 2d 69 20 3c 71 75 69 6b 72 5f 6f 74 75 3e 2e 62 69 6f 6d 20 2d 6d 20 77 65 | ity.py.-i.<quikr_otu>.biom.-m.we |
| 3bc0 | 69 67 68 74 65 64 5f 75 6e 69 66 72 61 63 20 2d 6f 20 62 65 74 61 5f 64 69 76 20 2d 74 20 3c 74 | ighted_unifrac.-o.beta_div.-t.<t |
| 3be0 | 72 65 65 20 66 69 6c 65 3e 20 28 65 78 61 6d 70 6c 65 3a 20 72 64 70 37 5f 6d 61 66 66 74 2e 66 | ree.file>.(example:.rdp7_mafft.f |
| 3c00 | 61 73 74 74 72 65 65 29 3e 00 20 20 20 20 63 6f 6e 76 65 72 74 5f 62 69 6f 6d 2e 70 79 20 2d 69 | asttree)>.....convert_biom.py.-i |
| 3c20 | 20 3c 71 75 69 6b 72 5f 6f 74 75 5f 74 61 62 6c 65 2e 74 78 74 3e 20 2d 6f 20 3c 71 75 69 6b 72 | .<quikr_otu_table.txt>.-o.<quikr |
| 3c40 | 5f 6f 74 75 3e 2e 62 69 6f 6d 20 2d 2d 62 69 6f 6d 5f 74 61 62 6c 65 5f 74 79 70 65 3d 22 6f 74 | _otu>.biom.--biom_table_type="ot |
| 3c60 | 75 20 74 61 62 6c 65 22 00 00 54 68 65 20 51 49 49 4d 45 20 70 72 6f 63 65 64 75 65 3a 00 00 33 | u.table"..The.QIIME.procedue:..3 |
| 3c80 | 2e 20 79 6f 75 72 2d 64 65 66 69 6e 65 64 20 71 69 69 6d 65 5f 6d 65 74 61 64 61 74 61 5f 66 69 | ..your-defined.qiime_metadata_fi |
| 3ca0 | 6c 65 2e 74 78 74 20 28 20 61 20 51 69 69 6d 65 20 4d 61 70 20 66 69 6c 65 29 00 20 20 20 67 67 | le.txt.(.a.Qiime.Map.file)....gg |
| 3cc0 | 5c 5f 39 34 5c 5f 6f 74 75 73 5c 5f 34 66 65 62 32 30 31 31 2e 74 72 65 2c 20 65 74 63 2e 29 00 | \_94\_otus\_4feb2011.tre,.etc.). |
| 3ce0 | 32 2e 20 74 68 65 20 74 72 65 65 20 6f 66 20 74 68 65 20 64 61 74 61 62 61 73 65 20 73 65 71 75 | 2..the.tree.of.the.database.sequ |
| 3d00 | 65 6e 63 65 73 20 74 68 61 74 20 77 65 72 65 20 75 73 65 64 20 28 65 2e 67 2e 20 20 64 70 37 5c | ences.that.were.used.(e.g...dp7\ |
| 3d20 | 5f 6d 61 66 66 74 2e 66 61 73 74 74 72 65 65 2c 00 31 2e 20 71 75 69 6b 72 5f 6f 74 75 5f 74 61 | _mafft.fasttree,.1..quikr_otu_ta |
| 3d40 | 62 6c 65 2e 74 78 74 20 28 54 68 65 20 4f 54 55 20 54 61 62 6c 65 20 67 65 6e 65 72 61 74 65 64 | ble.txt.(The.OTU.Table.generated |
| 3d60 | 20 77 69 74 68 20 6d 75 6c 74 69 66 61 73 74 61 5f 74 6f 5f 6f 74 75 00 00 50 72 65 2d 72 65 71 | .with.multifasta_to_otu..Pre-req |
| 3d80 | 75 69 73 69 74 65 73 3a 00 00 55 6e 77 65 69 67 68 74 65 64 2e 29 00 28 4e 6f 74 65 3a 20 4f 75 | uisites:..Unweighted.).(Note:.Ou |
| 3da0 | 72 20 63 6f 64 65 20 77 6f 72 6b 73 20 6d 75 63 68 20 62 65 74 74 65 72 20 77 69 74 68 20 57 45 | r.code.works.much.better.with.WE |
| 3dc0 | 49 47 48 54 45 44 20 55 6e 69 66 72 61 63 20 61 73 20 6f 70 70 6f 73 65 64 20 74 6f 00 34 2d 73 | IGHTED.Unifrac.as.opposed.to.4-s |
| 3de0 | 74 65 70 20 51 49 49 4d 45 20 70 72 6f 63 65 64 75 72 65 20 61 66 74 65 72 20 75 73 69 6e 67 20 | tep.QIIME.procedure.after.using. |
| 3e00 | 51 75 69 6b 72 20 74 6f 20 6f 62 74 61 69 6e 20 33 44 20 50 43 6f 41 20 67 72 61 70 68 73 3a 00 | Quikr.to.obtain.3D.PCoA.graphs:. |
| 3e20 | 00 20 20 73 61 6d 70 6c 65 20 66 61 73 74 61 20 66 69 6c 65 20 70 72 65 66 69 78 20 6e 61 6d 65 | ...sample.fasta.file.prefix.name |
| 3e40 | 73 00 2a 20 4e 6f 74 65 3a 20 57 68 65 6e 20 6d 61 6b 69 6e 67 20 79 6f 75 72 20 51 49 49 4d 45 | s.*.Note:.When.making.your.QIIME |
| 3e60 | 20 4d 65 74 61 64 61 74 61 20 66 69 6c 65 2c 20 74 68 65 20 73 61 6d 70 6c 65 20 69 64 27 73 20 | .Metadata.file,.the.sample.id's. |
| 3e80 | 6d 75 73 74 20 6d 61 74 63 68 20 74 68 65 00 00 23 23 23 20 50 6f 73 74 2d 70 72 6f 63 65 73 73 | must.match.the..###.Post-process |
| 3ea0 | 69 6e 67 20 6f 66 20 4d 75 6c 74 69 66 61 73 74 61 5c 5f 74 6f 5c 5f 6f 74 75 20 20 23 23 23 00 | ing.of.Multifasta\_to\_otu..###. |
| 3ec0 | 00 20 20 20 20 2d 56 2c 20 2d 2d 76 65 72 73 69 6f 6e 20 20 70 72 69 6e 74 20 76 65 72 73 69 6f | .....-V,.--version..print.versio |
| 3ee0 | 6e 2e 00 20 20 20 20 2d 76 2c 20 2d 2d 76 65 72 62 6f 73 65 20 76 65 72 62 6f 73 65 20 6d 6f 64 | n......-v,.--verbose.verbose.mod |
| 3f00 | 65 2e 00 20 20 20 20 69 73 20 63 6f 6d 70 61 74 69 62 6c 65 20 77 69 74 68 20 51 49 49 4d 45 27 | e......is.compatible.with.QIIME' |
| 3f20 | 73 20 63 6f 6e 76 65 72 74 5f 62 69 6f 6d 2e 70 79 20 28 6f 72 20 61 20 73 65 71 75 65 6e 63 65 | s.convert_biom.py.(or.a.sequence |
| 3f40 | 20 74 61 62 6c 65 20 69 66 20 6e 6f 74 20 4f 54 55 27 73 29 00 20 20 20 20 2d 6f 2c 20 2d 2d 6f | .table.if.not.OTU's).....-o,.--o |
| 3f60 | 75 74 70 75 74 20 74 68 65 20 4f 54 55 20 74 61 62 6c 65 2c 20 77 69 74 68 20 4e 55 4d 5f 52 45 | utput.the.OTU.table,.with.NUM_RE |
| 3f80 | 41 44 53 5f 50 52 45 53 45 4e 54 20 66 6f 72 20 65 61 63 68 20 73 61 6d 70 6c 65 20 77 68 69 63 | ADS_PRESENT.for.each.sample.whic |
| 3fa0 | 68 20 00 20 20 20 20 2d 6a 2c 20 2d 2d 6a 6f 62 73 20 73 70 65 63 69 66 69 65 73 20 68 6f 77 20 | h......-j,.--jobs.specifies.how. |
| 3fc0 | 6d 61 6e 79 20 6a 6f 62 73 20 74 6f 20 72 75 6e 20 61 74 20 6f 6e 63 65 2e 20 28 64 65 66 61 75 | many.jobs.to.run.at.once..(defau |
| 3fe0 | 6c 74 20 76 61 6c 75 65 20 69 73 20 74 68 65 20 6e 75 6d 62 65 72 20 6f 66 20 43 50 55 73 29 00 | lt.value.is.the.number.of.CPUs). |
 |
index : quikr.git | |
| Quikr - a bio classifier based on NNLS |
| aboutsummaryrefslogtreecommitdiff |
blob: 428a3b65fa89d19d7dbaa6c0cc3f45399a305c75 (plain)