NAME

       mirabait - select reads from a read collection

SYNOPSIS

       mirabait    [-f    <fromtype>]    [-t    <totype>   [-t   <totype>   ...]]   [-iklor]   baitfile   infile
       <basename_for_outfile(s)>

DESCRIPTION

       mirabait 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.

OPTIONS

       -f <fromtype>
              load this type of project files, where fromtype is:

       caf    sequences from CAF

       maf    sequences from MAF

       phd    sequences from a PHD

       gbf    sequences from a GBF

       fasta  sequences from a FASTA

       fastq  sequences from a FASTQ

       -t <totype>
              write the sequences to this type (multiple mentions of -t are allowed):

       fasta  sequences to FASTA

       fastq  sequences to FASTQ

       caf    sequences to CAF

       maf    sequences to MAF

       txt    sequence names to text file

       -k     k-mer, length of bait in bases (<32, default=31)

       -n     Min. number of k-mer baits needed (default=1)

       -i     Inverse hit: writes only sequences that do not hit bait

       -r     No checking of reverse complement direction

       -o     fastq quality Offset (only for -f = 'fastq') Offset of quality values in FASTQ file. Default: 33 A
              value of 0 tries to automatically recognise.

       -f <fromtype>
              load this type of project files, where fromtype is:

       caf    sequences from CAF

       maf    sequences from MAF

       phd    sequences from a PHD

       gbf    sequences from a GBF

       fasta  sequences from a FASTA

       fastq  sequences from a FASTQ

       -t <totype>
              write the sequences to this type (multiple mentions of -t are allowed):

       fasta  sequences to FASTA

       fastq  sequences to FASTQ

       caf    sequences to CAF

       maf    sequences to MAF

       txt    sequence names to text file

       -k     k-mer, length of bait in bases (<32, default=31)

       -n     Min. number of k-mer baits needed (default=1)

       -i     Inverse hit: writes only sequences that do not hit bait

       -r     No checking of reverse complement direction

       -o     fastq quality Offset (only for -f = 'fastq') Offset of quality values in FASTQ file. Default: 33 A
              value of 0 tries to automatically recognise.

AUTHOR

       Bastien Chevreux        (bach@chevreux.org)

MIRALIB version 3.9.18                             August 2013                                      MIRABAIT:(1)