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

FASTAQ-SEQUENCE_TRIM(1) User Commands FASTAQ-SEQUENCE_TRIM(1)

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
June 2017 fastaq 3.15.0