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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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  • person_outline Pjotr Prins

Publication for Sambamba

Sambamba citations

 (32)
library_books

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

2018
Nat Commun
PMCID: 5890265
PMID: 29632298
DOI: 10.1038/s41467-018-03724-9

[…] using bbduk2 included in bbmap (mink = 3 qtrim = r trimq = 10 minlength = 20). for the mapping to the reference genomes, we used bs-seeker2, relying on bowtie2 end-to-end alignments, and using sambamba rmdup to eliminate pcr duplicates. methylation calls were genotype corrected using read data from bs-seeker2 atcgmap output file. the scaffolds corresponding to plastid or mitochondrial […]

library_books

Performance comparison of three DNA extraction kits on human whole exome data from formalin fixed paraffin embedded normal and tumor samples

2018
PLoS One
PMCID: 5886566
PMID: 29621323
DOI: 10.1371/journal.pone.0195471

[…] as the ratio between the depth of the alternative allele (ad) and the total depth (dp). the ad and dp values were extracted from the vcf files. for the average gene coverage, we used the tool sambamba [] to calculate the read coverage for all the position of a given gene from the alignments files (option “depth base”)., we checked the dna quality for all samples by measuring the dna […]

library_books

Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

2018
BMC Genomics
PMCID: 5831853
PMID: 29490606
DOI: 10.1186/s12864-018-4558-4

[…] genome version 2 (ncbi assembly #gca_000004515.3) using burrows-wheeler alignment (bwa version 0.7.12-r1039) with the options –a –m –r followed by variant calling with samtools version 1.2.1 [], sambamba version 0.6.4 [] and bcftools version 1.2.1 []. bam files were then pooled and variants filtered with vcftools version 0.1.15 [] to maintain only biallelic sites with an overall mapping […]

library_books

Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cells of origin

2018
Nat Commun
PMCID: 5805678
PMID: 29422656
DOI: 10.1038/s41467-018-03025-1

[…] 1000 genomes project including decoy sequences) using the burrows-wheele aligner (bwa) version 0.7.15 mem function with default parameters (except for invoking -t 0),. duplicates were marked with sambamba version 0.6.5. single-nucleotide variations (snvs) and insertions/deletions (indels) were called using an in-house workflow, based on samtools/bcftools 0.1.19 (for snvs) and platypus 0.8.1 […]

library_books

A recurrent de novo missense mutation in UBTF causes developmental neuroregression

2018
Hum Mol Genet
PMCID: 5886272
PMID: 29300972
DOI: 10.1093/hmg/ddx435

[…] pipeline and axeq technologies. wes quality was verified by using picard (http://broadinstitute.github.io/picard/). wes quality for udp_2009, udp_7621, and udp_5762 was assessed by conjointly using sambamba 0.6.6 () and shell scripts. sequence data were aligned to human reference genome (hg19) using novoalign (novocraft technologies). the quality of alignment and genotype call of variants […]

library_books

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

2017
Genome Biol Evol
PMCID: 5786231
PMID: 29281015
DOI: 10.1093/gbe/evx276

[…] ). for each accession, we aligned the 76 or 100 bp illumina paired-end reads with bwa-mem (standard settings, ) to version 2.0 of the b. distachyon reference genome. after removing duplicates with sambamba (), single nucleotide polymorphisms were called with freebayes (). standard settings were used for both programs. the following filters were applied to the raw freebayes output: we first […]


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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.