This is the command mirabait that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
Use mirabait online using onworks.net services
