From: Daniel Jones Date: Fri, 18 Nov 2011 20:26:43 +0000 (-0800) Subject: README clarifications. X-Git-Url: https://git.donarmstrong.com/?p=fastq-tools.git;a=commitdiff_plain;h=33821bf1e64a562efa4507c7b3a7d88344db2f07 README clarifications. --- diff --git a/README b/README deleted file mode 100644 index ad14efe..0000000 --- a/README +++ /dev/null @@ -1,69 +0,0 @@ - -fastq-tools -=========== - -This package provides a number of small and efficient programs to perform common -tasks with high throughput sequencing data in the FASTQ format. All of the -programs work with typical FASTQ files as well as gzipped FASTQ files. - - -index ------ - -The following programs are provided. See the individual man pages for more -information. - - -*fastq-grep* : match sequences against regular expressions - -*fastq-kmers* : count k-mer occurrences - -*fastq-match* : (smith-waterman) local sequence alignment - -*fastq-uniq* : count duplicate reads - - -install -------- - -On most systems, this is a simple `./configure && make install`. - -The only external dependencies are PCRE (http://www.pcre.org/) and zlib -(http://zlib.net/). - - -contribute ----------- - -If you have written any small but useful programs to deal with FASTQ files, -please consider submitting them for inclusion in fastq-tools. Check out the -Github page (https://github.com/dcjones/fastq-tools) or send mail to the author -(dcjones@cs.washington.edu). - - -copying -------- - -This package is provided under a permissive MIT-style license. In particular: - -Copyright (C) 2011 by Daniel C. Jones - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. - - diff --git a/README.md b/README.md new file mode 100644 index 0000000..75a28d3 --- /dev/null +++ b/README.md @@ -0,0 +1,77 @@ + +fastq-tools +=========== + +This package provides a number of small and efficient programs to perform common +tasks with high throughput sequencing data in the FASTQ format. All of the +programs work with typical FASTQ files as well as gzipped FASTQ files. + + +index +----- + +The following programs are provided. See the individual man pages for more +information. + + +* *fastq-grep* : match sequences against regular expressions + +* *fastq-kmers* : count k-mer occurrences + +* *fastq-match* : (smith-waterman) local sequence alignment + +* *fastq-qual* : tabulate quality scores + +* *fastq-sample* : randomly sample reads, with or without replacement + +* *fastq-uniq* : count duplicate reads + + + +install +------- + +On most systems, installation is as simple as `./configure && make install`. + +If the source was obtained from the git repository, the included `./autogen.sh` +script must be run first to generate the `configure` script. + +The only external dependencies are PCRE (http://www.pcre.org/) and zlib +(http://zlib.net/). + + +contribute +---------- + +If you have written any small but useful programs to deal with FASTQ files, +please consider submitting them for inclusion in fastq-tools. Check out the +Github page (https://github.com/dcjones/fastq-tools) or send mail to the author +(dcjones@cs.washington.edu). + + +copying +------- + +This package is provided under a permissive MIT-style license. In particular: + +Copyright (C) 2011 by Daniel C. Jones + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + +