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
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