.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH FASTAQ-SEQUENCE_TRIM "1" "December 2023" "fastaq_sequence_trim 3.17.0" "User Commands"
.SH NAME
fastaq_sequence_trim \- Trim exact matches to a given string off the start of every sequence
.SH DESCRIPTION
usage: fastaq_sequence_trim [options] <infile_1> <infile_2> <outfile_1> <outfile_2> <trim_seqs>
.PP
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
.SS "positional arguments:"
.TP
infile_1
Name of forward fasta/q file to be trimmed
.TP
infile_2
Name of reverse fasta/q file to be trimmed
.TP
outfile_1
Name of output forward fasta/q file
.TP
outfile_2
Name of output reverse fasta/q file
.TP
trim_seqs
Name of file of sequences to search for at the start of
each input sequence
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-min_length\fR INT
Minimum length of output sequences [50]
.TP
\fB\-\-revcomp\fR
Trim the end of each sequence if it matches the reverse
complement. This option is intended for PCR primer
trimming