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- Gregory G. Faust
- 1 1Department of Biochemistry and Molecular Genetics and 2Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
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- Ira M. Hall
- 1 1Department of Biochemistry and Molecular Genetics and 2Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
説明
<jats:p>Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times.</jats:p> <jats:p>Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results.</jats:p> <jats:p>Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster.</jats:p> <jats:p>Contact: imh4y@virginia.edu</jats:p>
収録刊行物
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- Bioinformatics
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Bioinformatics 30 (17), 2503-2505, 2014-05-07
Oxford University Press (OUP)
