diff options
| author | Calvin <calvin@EESI> | 2013-05-14 21:51:40 -0400 |
|---|---|---|
| committer | Calvin <calvin@EESI> | 2013-05-14 21:51:40 -0400 |
| commit | 0773aaf89678b967588a902df1f5e6f9ccea393d (patch) | |
| tree | 40762e5df1da876d460d8695357ab0835645e8c6 /src/c/quikr.1 | |
| parent | 1d2becc9af591d37badfe0e77751bbb80932472f (diff) | |
release1.0
Diffstat (limited to 'src/c/quikr.1')
| -rw-r--r-- | src/c/quikr.1 | 70 |
1 files changed, 70 insertions, 0 deletions
diff --git a/src/c/quikr.1 b/src/c/quikr.1 new file mode 100644 index 0000000..9982d94 --- /dev/null +++ b/src/c/quikr.1 @@ -0,0 +1,70 @@ +.TH quikr 1 quikr-2013-05 +.SH NAME +quikr \- Calculate estimated frequencies of bacteria in a sample. +.SH SYNOPSIS +.B quikr +.RB [ \-i +.IR input] +.RB [ \-f +.IR sensing-fasta] +.RB [ \-s +.IR sensing-matrix] +.RB [ \-l +.IR lambda ] +.RB [ \-k +.IR kmer ] +.RB [ \-o +.IR output ] +.RB [ \-v ] +.P +.BR quikr " ..." +.SH DESCRIPTION +.B quikr +Quikr returns the estimated frequencies of batcteria present when given a +input FASTA file and a trained sensing matrix +.P +.SH OPTIONS +.TP +.B \-i, --input +the sample's fasta file of NGS. READS (fasta format) +.TP +.B \-f, --sensing-fasta +location of the fasta file database used to create the sensing matrix. (fasta format) +.TP +.B \-s, --sensing-matrix +location of the sensing matrix. (trained from quikr_train) +.TP +.B \-k, --kmer +specify what size of kmer to use. (default value is 6) +.TP +.B \-l, --lambda +lambda value to use. (default value is 10000) +.TP +.B \-o, --output +OTU_FRACTION_PRESENT a vector representing the percentage of database sequence's presence in sample. (csv output) +.TP +.B \-v, --verbose +verbose mode. +.SH EXAMPLES +Use quikr to calculate the estimated frequencies for sample.fa, using rdp7.fasta as the sensing matrix we generated with quikr_train. This uses 6-mers by default, and a lambda value of 10000: +.P +quikr -i sample.fa -f rdp7.fa -s rdp_sensing_matrix.gz -o frequencies.txt +.SH "SEE ALSO" +\fBmultifasta_to_otu\fP(1), \fBquikr_train\fP(1). +.SH AUTHORS +.B quikr +was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison +<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, Jean-Luc Bouchot +.SH REPORTING BUGS +.TP +Please report all bugs to Gail Rosen <gailr@ece.drexel.edu>. Include your \ +operating system, current compiler, and test files to reproduce your issue. +.SH COPYRIGHT. +Copyright \(co 2013 by Calvin Morrison and Gail Rosen. Permission to use, +copy, modify, distribute, and sell this software and its documentation for +any purpose is hereby granted without fee, provided that the above copyright +notice appear in all copies and that both that copyright notice and this +permission noticeappear in supporting documentation. No representations are +made about the suitability of this software for any purpose. It is provided +"as is" without express or implied warranty. + |