NAME

fastq-grep - print sequences matching a pattern

SYNOPSIS

fastq-grep [OPTION]... PATTERN [FILE]...

DESCRIPTION

Given a PATTERN, specified as a perl-compatible regular expression, print every FASTQ entry with a matching nucleotide sequence.

One or more FILEs may be specified, otherwise input is read from standard input.

OPTIONS

-i, --id

Match the read ID (by default, the sequence is matched).

-v, --invert-match

Invert the sense of matching, to select non-matching entries.

-m, --mismatches=FILE

Output non-matching entries to the given file.

-c, --count

Suppress normal output; instead output the number of matching (or, non-matching, with '-v') entries.

-h, --help

Output a help message and exit.

-V, --version

Output version information and exit.

AUTHOR

Written by Daniel C. Jones <dcjones@cs.washington.edu>