NAME
fastaq_sequence_trim - Trim exact matches to a given string off the start of every sequence
DESCRIPTION
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