.TH FASTQ-SAMPLE 1

.SH NAME
fastq-sample - sample random reads from a fastq file

.SH SYNOPSIS
.B fastq-sample [OPTION]... [[FILE] [FILE2]]

.SH DESCRIPTION
Given a FASTQ file, random reads are sampled and output, with or without
replacement, according to the '-r' option. The number of reads to sample can be
specifed with the '-n' option, or in terms of the proportion of total reads
using '-p' option.

If two files are given, the input is treated as paired-end, and matching pairs
are sampled and output into seperate files: [prefix].1.fastq and
[prefix].2.fastq, where [prefix] is set with the '-o' option.

.SH OPTIONS
.TP
\fB\-n N\fR
The number of reads to sample and output
.TP
\fB\-p N\fR
The number of reads to sample in terms of the proportion of total reads. If
sampling with replacement, this number may be greater than 1.0.
.TP
\fB\-o\fR, \fB\-\-output=PREFIX\fR
The filename prefix to which output should be written. If single-end data is
being sampled, the output file is [PREFIX].fastq, and with paired-end,
[PREFIX].1.fastq and [PREFIX].2.fastq.
.TP
\fB\-r\fR, \fB\-\-with\-replacement\fR
Sample with replacement. (By default, sampling is done without replacement.)
.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>