NAME

fastq-sort - sort entries in a fastq file

SYNOPSIS

fastq-sort [OPTION]... [FILE]...

DESCRIPTION

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

OPTIONS

-r, --reverse

Sort in reverse (i.e., descending) order.

-i, --id

Sort alphabetically by read identifier. -n, --idn Sort alphanumerically by read identifier.

-s, --seq

Sort alphabetically by nucleotide sequence.

-R, --random

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.

--seed=[SEED]

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.

-G, --gc

Sort by increasing GC-content.

-M, --mean-qual

Sort by increasing mean quality score.

-S, --buffer-size

Amount of memory to use while sorting. E.g., 1G, 250M, 200K, etc.

-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>