SAMBLASTER: fast duplicate marking and structural variant read extraction

@inproceedings{Faust2014SAMBLASTERFD,
  title={SAMBLASTER: fast duplicate marking and structural variant read extraction},
  author={Gregory G. Faust and Ira M. Hall},
  booktitle={Bioinformatics},
  year={2014}
}
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… CONTINUE READING
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