.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
.TH MIRABAIT: "1" "August 2013" "MIRALIB version 3.9.18" "User Commands"
.SH NAME
mirabait \- select reads from a read collection
.SH SYNOPSIS
.B mirabait
[\fI\-f <fromtype>\fR] [\fI\-t <totype> [\-t <totype> ...]\fR] [\fI\-iklor\fR] baitfile infile <basename_for_outfile(s)>
.SH DESCRIPTION
\fBmirabait\fR selects reads from a read collection which
are partly similar or equal to sequences defined as target
baits. Similarity is defined by finding a user-adjustable number of
common k-mers (sequences of k consecutive bases) which are the same in
the bait sequences and the screened sequences to be selected, either in forward
or reverse complement direction.
.SH OPTIONS
.TP
\fB\-f\fR <fromtype>
load this type of project files, where fromtype is:
.TP
caf
sequences from CAF
.TP
maf
sequences from MAF
.TP
phd
sequences from a PHD
.TP
gbf
sequences from a GBF
.TP
fasta
sequences from a FASTA
.TP
fastq
sequences from a FASTQ
.TP
\fB\-t\fR <totype>
write the sequences to this type (multiple mentions
of \fB\-t\fR are allowed):
.TP
fasta
sequences to FASTA
.TP
fastq
sequences to FASTQ
.TP
caf
sequences to CAF
.TP
maf
sequences to MAF
.TP
txt
sequence names to text file
.TP
\fB\-k\fR
k\-mer, length of bait in bases (<32, default=31)
.TP
\fB\-n\fR
Min. number of k\-mer baits needed (default=1)
.TP
\fB\-i\fR
Inverse hit: writes only sequences that do not hit bait
.TP
\fB\-r\fR
No checking of reverse complement direction
.TP
\fB\-o\fR
fastq quality Offset (only for \fB\-f\fR = 'fastq')
Offset of quality values in FASTQ file. Default: 33
A value of 0 tries to automatically recognise.
.TP
\fB\-f\fR <fromtype>
load this type of project files, where fromtype is:
.TP
caf
sequences from CAF
.TP
maf
sequences from MAF
.TP
phd
sequences from a PHD
.TP
gbf
sequences from a GBF
.TP
fasta
sequences from a FASTA
.TP
fastq
sequences from a FASTQ
.TP
\fB\-t\fR <totype>
write the sequences to this type (multiple mentions
of \fB\-t\fR are allowed):
.TP
fasta
sequences to FASTA
.TP
fastq
sequences to FASTQ
.TP
caf
sequences to CAF
.TP
maf
sequences to MAF
.TP
txt
sequence names to text file
.TP
\fB\-k\fR
k\-mer, length of bait in bases (<32, default=31)
.TP
\fB\-n\fR
Min. number of k\-mer baits needed (default=1)
.TP
\fB\-i\fR
Inverse hit: writes only sequences that do not hit bait
.TP
\fB\-r\fR
No checking of reverse complement direction
.TP
\fB\-o\fR
fastq quality Offset (only for \fB\-f\fR = 'fastq')
Offset of quality values in FASTQ file. Default: 33
A value of 0 tries to automatically recognise.
.SH AUTHOR
Bastien Chevreux        (bach@chevreux.org)