NAME

fastq-match - print sequences matching a pattern

SYNOPSIS

fastq-match [OPTION]... QUERY [FILE]...

DESCRIPTION

Given a nucleotide sequence QUERY, perform local alignment against every FASTQ sequence using the Smith-Waterman algorithm. For each read, an alignment score is printed, so that the output consists of a simple list of scores.

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

OPTIONS

-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>