Sambamba protocols

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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 in pipelines

 (6)
2017
PMCID: 5266269
PMID: 28122052
DOI: 10.1371/journal.pone.0170632

[…] conditions. for categorical data,a fisher’s exact test was applied for each pair. for differences in means between the two conditions, a t-test was applied. pcr duplicates were calculated with sambamba []. the number of detected genes was calculated taking into account genes with at least one paired-end read mapped. the number of genes consuming 25% of the reads was calculated by ranking […]

2017
PMCID: 5411691
PMID: 28487883
DOI: 10.1101/mcs.a001610

[…] using a hardware-accelerated version of bwa (burrows–wheeler alignment) () version 0.7.8 mem with option -t 0. the sambamba package () version 0.4.6 and 0.5.9, respectively, was used for sorting and to mark polymerase chain reaction (pcr) duplicates during merging the per-lane bam (binary alignment) files., […]

2017
PMCID: 5591018
PMID: 28846694
DOI: 10.1371/journal.pgen.1006834

[…] on the y chromosome was found using http://www.ncbi.nlm.nih.gov/ along with 1 mb of x-degenerate region. the raw reads were mapped to these genes for each individual with bwa-mem and filtered using sambamba with the parameters mentioned above., cnvnator [] was used to call duplications and deletions using a binsize of 100 bp and gc correction. cnvnator was used in the whole gene except for daz […]

2017
PMCID: 5615344
PMID: 28837078
DOI: 10.3390/genes8090210

[…] human genome 19 (hg19) with decoy sequences [] with the default parameters, then duplicate reads were marked using biobambam2 []. the aligned reads were sorted by the genomic coordinate using sambamba processor [] and stored in bam format files. single nucleotide polymorphism (snps), short insertion-deletion (indels) and single nucleotide variant (snvs) calling was performed using genome […]

2016
PMCID: 4758756
PMID: 26891448
DOI: 10.1371/journal.ppat.1005438

[…] rna-seq analysis is shown in . while multiple tools were used for independent cross-validation at each step, the analysis reported here was done with a pipeline consisting of: star aligner > sambamba filter for unique reads > genomicalignments (within r) > deseq2 (within r) > ipathwayguide. a comparison of the output of differential expression analyses from multiple pipelines, […]

Sambamba in publications

 (30)
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 […]

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 […]

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 […]

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 […]

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 […]

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.