4 fastq-grep - print sequences matching a pattern
7 .B fastq-grep [OPTION]... PATTERN [FILE]...
10 Given a PATTERN, specified as a perl-compatible regular expression, print every
11 FASTQ entry with a matching nucleotide sequence.
13 One ore more FILEs may be specified, otherwise input is read from standard input.
17 \fB\-i\fR, \fB\-\-id\fR
18 Match the read ID (by default, the sequence is matched).
20 \fB\-v\fR, \fB\-\-invert\-match\fR
21 Invert the sense of matching, to select non-matching entries.
23 \fB\-m\fR, \fB\-\-mismatches=FILE\fR
24 Output non-matching entries to the given file.
26 \fB\-c\fR, \fB\-\-count\fR
27 Suppress normal output; instead output the number of matching (or, non-matching,
30 \fB\-h\fR, \fB\-\-help\fR
31 Output a help message and exit.
33 \fB\-V\fR, \fB\-\-version\fR
34 Output version information and exit.
37 Written by Daniel C. Jones <dcjones@cs.washington.edu>