NAME
fastaq_sequence_trim
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]
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.