Bioinformatics · 2015 · 2.7K citations · 7 references
Life SciencesBioinformaticsMolecular BiologyGenomic Data AnalysisGenomicsSequence AnalysisContig ConstructionDna SequencingNext-generation SequencingSequence AlignmentCoverage AnalysisFilteringMulti-core ComputingOpen-source Software Development
Sambamba is a high‑performance, multi‑core tool that processes SAM, BAM, and CRAM alignment files faster than samtools. The authors released Sambamba v0.5.0 (doi:10.5281/zenodo.13200), a freely available open‑source tool for NGS alignment processing. Sequencing centers adopt Sambamba for its speed and added features such as coverage analysis and powerful filtering. Sambamba is free and open source under GPLv2, downloadable from http://www.open-bio.org/wiki/Sambamba, with contact j.c.p.prins@umcutrecht.nl.
Abstract Summary: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. Sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability. Availability and implementation: Sambamba is free and open source software, available under a GPLv2 license. Sambamba can be downloaded and installed from http://www.open-bio.org/wiki/Sambamba. Sambamba v0.5.0 was released with doi:10.5281/zenodo.13200. Contact: j.c.p.prins@umcutrecht.nl
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The Sequence Alignment/Map format and SAMtools
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