Sambamba pipeline

Sambamba specifications

Information


Unique identifier OMICS_07586
Name Sambamba
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM, CRAM
Output format SAM, BAM, CRAM, BAI
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.5.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Pjotr Prins <>

Publication for Sambamba

Sambamba citations

 (2)
2017
PMCID: 5559527

[…] ca, usa)., de-multiplexing of raw sequencing data was performed using casava v.1.8.4 (illumina). reads were aligned to the human genome reference grch37 release 75 using bwa-mem version 0.7.1248. sambamba v0.5.649 was used to sort and index bam files and to mark duplicates. base recalibration and indel realignment were performed according to genome analysis toolkit (gatk) best practices […]

2016
PMCID: 4768167

[…] archive (ena): http://www.ebi.ac.uk/ena/data/view/prjeb9910., rna-seq reads were mapped with burrows-wheeler aligner 0.5.946 onto the rat reference genome rgsc5.0. the bam files were sorted with sambamba v0.5.147 and reads were counted with htseq-count version 0.6.0 (default settings)48 to exons as defined in rattus_norvegicus.rnor_5.0.74.gtf (ensembl). non-uniquely mapped reads […]

Sambamba institution(s)
Department of Statistical Simulation, St Petersburg State University, St Petersburg, Russia, Illumina Cambridge, Cambridge, UK; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands; Department of Medical Genetics, Institute for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands; Department of Nematology, Wageningen University, Wageningen, Netherlands

Sambamba review

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Maja Kuzman

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Desktop
Truly dramatic decrease in processing time for bam and sam files compared to samtools.