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Crossbow

Searches for single nucleotide polymorphisms (SNPs) with cloud computing. Crossbow is a Hadoop-based software tool that combines the speed of the short read aligner Bowtie with the accuracy of the SNP caller SOAPsnp to perform alignment and SNP detection for multiple whole-human datasets per day. The software achieves at least 98.9% accuracy on simulated datasets of individual chromosomes, and better than 99.8% concordance with the Illumina 1 M BeadChip assay of a sequenced individual.

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Crossbow classification

Crossbow specifications

Software type:
Framework/Library, Pipeline/Workflow
Restrictions to use:
None
Parallelization:
MapReduce
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
1.2.1
High performance computing:
Yes

Subtools

  • Bowtie
  • SoapSNP

Crossbow distribution

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Crossbow support

Documentation

Maintainer

  • Ben Langmead <>

Additional information

http://bowtie-bio.sourceforge.net/crossbow/manual.shtml

Credits

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Publications

Institution(s)

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; The iSchool, College of Information Studies, University of Maryland, College Park, MD, USA

Funding source(s)

Supported in part by NSF grant IIS-0844494, NIH grants R01-LM006845 and R01-HG004885.

Link to literature

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