SAMBLASTER: fast duplicate marking and structural variant read extraction
By Gregory G. Faust, Ira M. Hall. Bioinform., 2014
864 citations recorded by the source corpus.
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
Subfields: Artificial Intelligence, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/5565e44b8a7d3feefd1d40e6b028a1f5a17ca121
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Citations in the corpus
- Large-scale whole-genome sequencing of three diverse Asian populations in Singapore (2018, neutral): “22).(55) We sorted and merged aligned read pairs from different sequencing lanes using SAMtools (version 1.”
- PRIM1 deficiency causes a distinctive primordial dwarfism syndrome (2020, neutral): “Postprocessing was performed with samblaster (0.1.22) (Faust and Hall 2014) to mark duplicate reads, and the genome analysis toolkit (GATK, v3.”
- Sambamba: fast processing of NGS alignment formats (2015, background): “Samtools has inspired a number of other BAM processors, notably Picard (Picard, 2009), samblaster (Faust and Hall, 2014), biobambam (Tischler and Leonard, 2014) and Scramble (Bonfield, 2014), each of which is either slower than samtools, or offers a subset of its functionality.”