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)