Sambamba: fast processing of NGS alignment formats
By Artem Tarasov, Albert J. Vilella, Edwin Cuppen, I. Nijman, Pjotr Prins. Bioinform., 2015
2,070 citations recorded by the source corpus.
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
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/5f913c0c71e366cb3dcf2ee579fc00749cd9f6d4
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Ecology
- J. de Ridder
- Wigard P. Kloosterman
- Daniel C. Koboldt
- Shane A. McCarthy
- Heng Li
- Kathryn E. Holt
- Ryan R. Wick
- Louise M. Judd
In Molecular Biology
- Daniel C. Koboldt
- Aaron R. Quinlan
- Wigard P. Kloosterman
- J. de Ridder
- Tobias Marschall
- Shane A. McCarthy
- Brent S. Pedersen
- Edwin Cuppen
Citations in the corpus
- Twelve years of SAMtools and BCFtools (2020, methodology): “These include tools for file manipulation, quality control, and data analyses, such as sambamba[4], biobambam[5], FastQC[6], and GATK[7].”
- Best practices for variant calling in clinical sequencing (2020, methodology): “Marking duplicates Picard tools [28], Sambamba [29], SAMBLASTER [30]”
- Next-Generation Sequencing Technology: Current Trends and Advancements (2023, neutral): “Cont.”
- Mosdepth: quick coverage calculation for genomes and exomes (2017, background): “, 2009) outputs per-base coverage; BEDTools genomecov (Quinlan and Hall, 2010; Quinlan, 2014) can output per-region or per-base coverage; Sambamba (Tarasov et al., 2015) also provides per-base and per-window depth calculations.”
- Mapping and phasing of structural variation in patient genomes using nanopore sequencing (2017, positive): “Reads were realigned using GATK IndelRealigner 51 and deduplication was performed using Sambamba markdup 52 .”