.TH multifasta_to_otu 1 multifasta_to_otu-2013-05
.SH NAME
multifasta_to_otu \- create a QIIME OTU table based on Quikr results.
.SH SYNOPSIS
.B multifasta_to_otu
.RB [ \-i
.IR input-directory ]
.RB [ \-f
.IR sensing-fasta]
.RB [ \-s
.IR sensing-matrix]
.RB [ \-k
.IR kmer ]
.RB [ \-l
.IR lambda ]
.RB [ \-j
.IR jobs ]
.RB [ \-o
.IR otu-table]
.RB [ \-v ]
.P
.BR multifasta_to_otu " ..."
.SH DESCRIPTION
.B multifasta_to_otu
The multifasta_to_otu tool is a handy wrapper for quikr which lets the user
to input as many fasta files as they like, and then returns an OTU table of the
number of times a specimen was seen in all of the samples.
.P
.SH OPTIONS
.TP
.B \-i, --input-directory
the directory containing the samples' fasta files of reads (note each fasta file should correspond to a separate sample)
.TP
.B \-f, --sensing-fasta
location of the fasta file database used to create the sensing matrix.
.TP
.B \-s, --sensing-matrix
location of the sensing matrix.
.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 \-j, --jobs
specifies how many jobs to run at once. (default value is the number of CPUs)
.TP
.B \-o, --otu-table
the OTU table, with NUM_READS_PRESENT for each sample which is compatible with QIIME's convert_biom.py (or sequence table if not OTU's)
.TP
.B \-v, --verbose
verbose mode.
.SH USAGE
This program will use a large amount of memory, and CPU time. 
You can reduce the number of cores used, and thus memory, by specifying the -j flag with aspecified number of jobs. Otherwise multifasta_to_otu will run one job per cpu core.
.SH POSTPROCESSING
.B Note: When making your QIIME Metadata file, the sample id's must match the sample fasta file prefix names
.P
4-step QIIME procedure after using Quikr to obtain 3D PCoA graphs: (Note: Our code works much better with WEIGHTED Unifrac as opposed to Unweighted.)
.TP
Pre-requisites:
1. multifasta output file "quikr_output_table.txt" for our example.
.br
2. the tree of the database sequences that were used (e.g.dp7_mafft.fasttree, gg_94_otus_4feb2011.tre, etc.)
.br
3. your-defined <qiime_metadata_file.txt>
.TP
The QIIME procedue:
convert_biom.py -i <quikr_otu_table.txt> -o <quikr_otu>.biom --biom_table_type="otu table"
.br
beta_diversity.py -i <quikr_otu>.biom -m weighted_unifrac -o beta_div -t <tree file>
.br
principal_coordinates.py -i beta_div/weighted_unifrac_<quikr_otu>.txt -o <quikr_otu_project_name>_weighted.txt
.br
make_3d_plots.py -i <quikr_otu_project_name>_weighted.txt -o <3d_pcoa_plotdirectory> -m <qiime_metadata_file>
.SH "SEE ALSO"
\fBquikr\fP(1), \fBquikr_train\fP(1).
.SH AUTHORS
.B multifasta2otu 
was written by Gail Rosen <gailr@ece.drexel.edu>, Calvin Morrison 
<mutantturkey@gmail.com>, David Koslicki, Simon Foucart, and 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.