fastaq-sequence_trim1
Trim exact matches to a given string off the start of every sequence
Overview
usage: fastaq_sequence_trim [options] <infile_1> <infile_2> <outfile_1> <outfile_2> <trim_seqs>
Trims sequences off the start of all sequences in a pair of sequence 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:
infile_1
|
Name of forward fasta/q file to be trimmed |
|---|---|
infile_2
|
Name of reverse fasta/q file to be trimmed |
outfile_1
|
Name of output forward fasta/q file |
outfile_2
|
Name of output reverse fasta/q file |
trim_seqs
|
Name of file of sequences to search for at the start of each input sequence |
options:
-
-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
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.