Package: wnpp Severity: wishlist Owner: Andreas Tille <ti...@debian.org>
* Package name : jellyfish1 Version : 1.1.11 Upstream Author : Guillaume Marçais1, Carl Kingsford * URL : http://www.cbcb.umd.edu/software/jellyfish/ * License : BSD-like Programming Lang: C++ Description : count k-mers in DNA sequences JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This is the latest version of the 1.x series of jellyfish which is used by some other applications that are not compatible with version 2.x which is provided inside the jellyfish package. Remark: Jellyfish1 is no new package. It used to be in Debian but the code migrated to version 2 which is not compatible with all our tools. So there is a need to keep the latest release of version 1.x which is packaged here. The package is maintained by the Debian Med team at https://anonscm.debian.org/git/debian-med/jellyfish1.git