Human Genome Sequencing Center, Baylor College of Medicine

bang

Author:

K. James Durbin (Atlas Genome Tools Group)

bang

Is a fast repeat supressing search tool, written primarialy for anchoring reads to genomes, but also adaptable to other genome scale comparison problems.

bang's key features are efficiently coded k-mer hashing which gives it exceptional speed, a k-mer thinning scheme that allows it to run large jobs in comparatively small RAM footprint, and an ability to use k-mer distributions to effectively perform de novo repeat filtering of matches. bang is also designed to be convenient to use with even very large data sets (e.g. no arbitrary limits on the number of query sequences like megablast).

An example of the kind of performance you can expect form bang is given in the table below.

Program	GenomeSize	Reads	RAM	RunTime	Sensitivity	Specificity
bang	120 MB	500K (~450MB)	~400MB	10 minutes	0.981	0.973
megablast	120 MB	500K (~450MB)	~300MB	60 minutes	0.999	0.265
ssaha	120 MB	500K (~450MB)	? (ran out of memory on 4 GB machine)

This table gives out-of-the-box performance characteristics and is intended only to give you a relative view of the sort of characteristics bang has. Suitibility for any particular application is dependent on many factors.

To further illustrate the blinding speed of bang, consider a recent read mapping task we performed. In this task, 2.5 million human resequencing reads were mapped to the human genome using 8 cluster cpus in only 2.5 wall-clock hours, or a total of 18 cpu-hours. Peak RAM usage was 600 MB. Said another way, we could have done a complete mapping of 1x coverage of reads to the human genome on a single laptop in less than a day.

LICENSE

Please read the terms of the license agreement carefully.

License summary:

This software is made avaliable for internal research purposes only by individuals or employees of an academic institution or private company. Commercial production use or sale of software incorporating these libraries is prohibited. Commercial use licenses are available.

No part of this software, or modifications thereof, may be redistributed for any purpose to any other company, person, or individual, without prior written permission from the author.

This software is provided AS IS. Baylor College of Medicine assumes no responsibility or liability for damages of any kind that may result, directly or indirectly, from the use of this software.

SYSTEM REQUIREMENTS

Binaries available for Solaris, Linux x86, and OS X.
Compilation from source requires CBT++ library.

By downloading this software you explicitly agree to the terms of the license agreement .

Click to go to bang download page.

Contact James Durbin kdurbin@bcm.tmc.edu for information about obtaining a commercial license for this software.