.TH quikr_train 1 quikr_train-2013-05
.SH NAME
quikr_train \- train databases for use with Quikr
.SH SYNOPSIS
.B quikr_train
.RB [ \-i
.IR input]
.RB [ \-o
.IR output]
.RB [ \-k
.IR kmer ]
.RB [ \-v ]
.P
.BR quikr " ..."
.SH DESCRIPTION
.B quikr
The quikr_train is a utility to train a database for use with quikr.
Before running the quikr utility, you need to generate the sensing matrix or
download a pretrained one from our project's homepage.

quikr_train returns a sensing matrix that can be used with the quikr
function. 
.P
.SH OPTIONS
.TP
.B \-i, --input
the database of sequences to create the sensing matrix. (fasta format)
.TP
.B \-k, --kmer
specify what size of kmer to use. (default value is 6)
.TP
.B \-o, --output
the sensing matrix. (a gzip'd text file)
.TP
.B \-v, --verbose
verbose mode.
.SH EXAMPLES
Use quikr_train to generate a sensing matrix from rdp7.fasta. This uses 6mers by default.
.P
quikr_train -i rdp7.fa -o rd7_sensing_matrix.gz
.SH USAGE
If you do not have a .gz file on your output matrix name, it will be appended.
.SH "SEE ALSO"
\fBmultifasta_to_otu\fP(1), \fBquikr\fP(1).
.SH AUTHORS
.B quikr
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.