aq-mkrepset.1

.\" Authors: Andre Masella
.TH aq-mkrepset 1 "October 2011" "1.2" "USER COMMANDS"
.SH NAME 
aq-mkrepset \- Create a representative set of sequences
.SH SYNOPSIS
.B aq-mkrepset
.I seq.fasta
.I seq_otus.txt
.SH DESCRIPTION
Create a representative set as a replacement for \fBpick_rep_set.py\fR in QIIME. The QIIME version loads the entire FASTA file into a Python dictonary, which is unmanageable for large data sets. Instead, this version creates an index over the FASTA file, loads only the sequences in a single OTU and picks the mode (or randomly from the modes if there are multiple modes). This is much faster when the sets are large as it reduced memory usage and swapping.
.SH OPTIONS
.TP
seq.fasta
The original FASTA sequences.
.TP
seq_otus.txt
The clusters produced by \fBpick_otus.py\fR.
.SH SEE ALSO
.BR axiome (1).