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)
