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mirabait - Online in the Cloud

Run mirabait in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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.

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