5 This package provides a number of small and efficient programs to perform common
6 tasks with high throughput sequencing data in the FASTQ format. All of the
7 programs work with typical FASTQ files as well as gzipped FASTQ files.
13 The following programs are provided. See the individual man pages for more
17 * *fastq-grep* : match sequences against regular expressions
19 * *fastq-kmers* : count k-mer occurrences
21 * *fastq-match* : (smith-waterman) local sequence alignment
23 * *fastq-qual* : tabulate quality scores
25 * *fastq-sample* : randomly sample reads, with or without replacement
27 * *fastq-uniq* : count duplicate reads
29 * *fastq-qualadj* : adjust quality scores by a fixed offset
35 On most systems, installation is as simple as `./configure && make install`.
37 If the source was obtained from the git repository, the included `./autogen.sh`
38 script must be run first to generate the `configure` script.
40 The only external dependencies are PCRE (http://www.pcre.org/) and zlib
47 If you have written any small but useful programs to deal with FASTQ files,
48 please consider submitting them for inclusion in fastq-tools. Check out the
49 Github page (https://github.com/dcjones/fastq-tools) or send mail to the author
50 (dcjones@cs.washington.edu).
56 This package is provided under a permissive MIT-style license. In particular:
58 Copyright (C) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
60 Permission is hereby granted, free of charge, to any person obtaining a copy
61 of this software and associated documentation files (the "Software"), to deal
62 in the Software without restriction, including without limitation the rights
63 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
64 copies of the Software, and to permit persons to whom the Software is
65 furnished to do so, subject to the following conditions:
67 The above copyright notice and this permission notice shall be included in
68 all copies or substantial portions of the Software.
70 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
71 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
72 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
73 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
74 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
75 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN