fastaq_chunker (1)

fastaq_chunker [options] <fasta/q in> <prefix of output files> <chunk size> <tolerance>

Splits a multi fasta/q file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk_size chunks in each file, but allows a little extra, so chunk can be up to (chunk_size + tolerance), to prevent tiny chunks made from the ends of sequences

positional arguments:

infile

Name of input fasta/q file to be split

outprefix

Name of output fasta/q file

chunk_size

Size of each chunk

tolerance

Tolerance allowed in chunk size

optional arguments:

-h, --help

show this help message and exit

--skip_all_Ns

Do not output any sequence that consists of all Ns

fastaq_chunker was originally written by Martin Hunt ([email protected])

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.