BW4SA – Burrows-Wheeler Transform for Sequence Analysis

BW4SA

:: DESCRIPTION

BW4SA is a generic, practical, versatile library for implementing a variety of (bio)sequence analysis algorithms in succinct space.

::DEVELOPER

GSA (Genome-scale algorithmics) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BW4SA

:: MORE INFORMATION

Citation

Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
Versatile succinct representations of the bidirectional Burrows-Wheeler transform.
ESA 2013, Springer, Lecture Notes in Computer Science Volume 8125, 2013, pp 133-144

BEETL 1.1.0 – Burrows-Wheeler Extended Tool Library

BEETL 1.1

:: DESCRIPTION

BEETL is a suite of applications for building and manipulating the Burrows-Wheeler Transform (BWT) of collections of DNA sequences. The algorithms employed in BEETL are intended to scale to collections of sequences containing one billion entries or more.

::DEVELOPER

BEETL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BEETL

:: MORE INFORMATION

Citation

BEETL-fastq: a searchable compressed archive for DNA reads.
Janin L, Schulz-Trieglaff O, Cox AJ.
Bioinformatics. 2014 Jun 20. pii: btu387.

BMC Bioinformatics. 2013;14 Suppl 5:S2. doi: 10.1186/1471-2105-14-S5-S2. Epub 2013 Apr 10.
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.
Ander C1, Schulz-Trieglaff OB, Stoye J, Cox AJ.

BWA 0.7.17 – Burrows-Wheeler Aligner for Short and Long Reads.

BWA 0.7.17

:: DESCRIPTION

BWA (Burrows-Wheeler Aligner) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer sequences up to around 100kbp. Both algorithms do gapped alignment.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BWA

:: MORE INFORMATION

Citation:

Li H. and Durbin R. (2009)
Fast and accurate short read alignment with Burrows-Wheeler Transform.
Bioinformatics, 25:1754-60.

iBWA 0.6.2 – Iterative Burrows-Wheeler Alignment

iBWA 0.6.2

:: DESCRIPTION

iBWA is a fork of Heng Li’s BWA aligner with support for iteratively adding alternate haplotypes, reference patches, and variant hypotheses. This enables you to leverage existing tools and pipelines in the diverse BWA ecosystem while also creating new analysis opportunities.

::DEVELOPER

The Genome Institute at Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C compiler

:: DOWNLOAD

iBWA

:: MORE INFORMATION