DOKK / manpages / debian 10 / fastaq / fastaq-sequence_trim.1.en
FASTAQ-SEQUENCE_TRIM(1) User Commands FASTAQ-SEQUENCE_TRIM(1)

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

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

Name of forward fasta/q file to be trimmed
Name of reverse fasta/q file to be trimmed
Name of output forward fasta/q file
Name of output reverse fasta/q file
Name of file of sequences to search for at the start of each input sequence

show this help message and exit
Minimum length of output sequences [50]
Trim the end of each sequence if it matches the reverse complement. This option is intended for PCR primer trimming
July 2018 fastaq 3.17.0