SAMBLASTER: fast duplicate marking and structural variant read extraction

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ID: 302117
2014
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Abstract
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. 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. Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster. Contact: imh4y@virginia.edu
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openalex_W2132378736 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Gregory G. Faust, Ira M. Hall
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Journal BMC Bioinformatics
Year 2014
DOI
10.1093/bioinformatics/btu314
URL
https://academic.oup.com/bioinformatics/article-pdf/30/17/2503/48927353/bioinformatics_30_17_2503.pdf
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