fastq_quality_trimmer1

Overview

usage: fastq_quality_trimmer [-h] [-v] [-t N] [-l N] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit 0.0.13.1 by A. Gordon ([email protected])

[-h]

= This helpful help screen.

[-t N]

= Quality threshold - nucleotides with lower

quality will be trimmed (from the end of the sequence).

[-l N]

= Minimum length - sequences shorter than this (after trimming)

will be discarded. Default = 0 = no minimum length.

[-z]

= Compress output with GZIP.

[-i INFILE]

= FASTQ input file. default is STDIN.

[-o OUTFILE] = FASTQ output file. default is STDOUT. [-v] = Verbose - report number of sequences.

If [-o] is specified,

report will be printed to STDOUT.

If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.