SAMBLASTER: fast duplicate marking and structural variant read extraction

Bioinformatics. 2014 Sep 1;30(17):2503-5. doi: 10.1093/bioinformatics/btu314. Epub 2014 May 7.


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

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genomic Structural Variation*
  • Genomics / methods
  • Sequence Alignment
  • Sequence Analysis, DNA / methods*
  • Software*