DESCRIPTION

 fastaq_sequence_trim [options] <fasta/q 1 in> <fastaq/2 in> <out 1> <out 2> <trim_seqs>

Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming

positional arguments:

fasta/q 1 in

Name of forward fasta/q file to be trimmed

fasta/q 2 in

Name of reverse fasta/q file to be trimmed

out_1

Name of output forward fasta/q file

out_2

Name of output reverse fasta/q file

trim_seqs

Name of fasta/q file of sequences to search for at the start of each input sequence

optional arguments:

-h, --help

show this help message and exit

--min_length INT

Minimum length of output sequences [50]

--revcomp

Trim the end of each sequence if it matches the reverse complement. This option is intended for PCR primer trimming

AUTHOR

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

COPYING

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.