X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;fp=README.md;h=0000000000000000000000000000000000000000;hb=f203be083fa831bf53d01a9c1481d2ba8f646638;hp=b4cff423df9c44cfee6f2492480b74226742e0bc;hpb=63ab5aff4685ba7502fcc0c1a0045ce88a250af1;p=fastq-tools.git diff --git a/README.md b/README.md deleted file mode 100644 index b4cff42..0000000 --- a/README.md +++ /dev/null @@ -1,79 +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-sort* : sort fastq entries by various keys - -* *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 - -* *fastq-qualadj* : adjust quality scores by a fixed offset - - -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. - -