BSD Portswip/jellyfish2 2.2.10 NetBSD
Fast, memory-efficient counting of k-mers in DNA
- System
- NetBSD
- Repository
- pkgsrc-wip
- Maintainer
- [email protected]
- License
- gnu-gpl-v3
- Categories
- wip, biology
Description
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 quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
Install
From pkgsrc-wip (no binary package):
cd /usr/pkgsrc/wip/jellyfish2 && make install cleanDependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.