SlideSort

C++ implementation of SlideSort

Summary

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.

Installation

git clone https://github.com/iskana/SlideSort.git
cd SlideSort
/bin/sh mkall_v1.sh
/bin/sh mkall_v2.sh

Quick start with a sample file

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 Notice

Copyright (C) 2016, Kana Shimizu All rights reserved.

License

See the readme included in this repository.

Contact Information

• Kana Shimizu (shimizu.kana@waseda.jp)

History

2016/July/20; initial upload