.TH FASTQ-SORT 1

.SH NAME
fastq-sort - sort entries in a fastq file

.SH SYNOPSIS
.B fastq-sort [OPTION]... [FILE]...

.SH DESCRIPTION
Sort a FASTQ file, outputing the sorted file to standard out. If no files are
given, read from standard input.

.SH OPTIONS
.TP
\fB\-r\fR, \fB\-\-reverse\fR
Sort in reverse (i.e., descending) order.
.TP
\fB\-I\fR, \fB\-\-id\fR
Sort alphabetically by read identifier.
.TP
\fB\-S\fR, \fB\-\-seq\fR
Sort alphabetically by nucleotide sequence.
.TP
\fB\-R\fR, \fB\-\-random\fR
Sort in random order. By default, a fixed seed is used so that random sort is
deterministic. Use the '--seed' option to produce different random orderings on
repeated runs.
.TP
\fB\-\-seed=[SEED]\fR
If a decimal integer SEED is given, it is used as the seed when producing a
random ordering. With no argument, a seed is generated using the current system
time.
.TP
\fB\-G\fR, \fB\-\-gc\fR
Sort by increasing GC-content.
.TP
\fB\-M\fR, \fB\-\-mean-qual\fR
Sort by increasing mean quality score.
.TP
\fB\-h\fR, \fB\-\-help\fR
Output a help message and exit.
.TP
\fB\-V\fR, \fB\-\-version\fR
Output version information and exit.

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