C++ implementation of SlideSort
This library provides the implementation of the SlideSort and a related clustering tool [1].
- [1] Shimizu K, Tsuda K, SlideSort: All pairs similarity search for short reads. Bioinformatics, 2011: 27 (4): 464-470.
git clone https://github.com/iskana/SlideSort.git
cd SlideSort
/bin/sh mkall_v1.sh
/bin/sh mkall_v2.sh
Enumerating all similar pairs:
cd SlideSort/SS_v2
./slidesort_v2 -d 3 -i test.fasta -mt 4
or
cat test.fasta| ./slidesort_v2 -d 3 -I -mt 4
Finding MSTs:
cd SlideSort/mst_v2
./ssmst_v2 -d 3 -i test.fasta -mt 4
or
cat test.fasta| ./ssmst_v2 -d 3 -I -mt 4 -Z
Copyright (C) 2016, Kana Shimizu All rights reserved.
See the readme included in this repository.
- Kana Shimizu (shimizu.kana@waseda.jp)
2016/July/20; initial upload