Sambamba: fast processing of NGS alignment formats
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Summary
Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time, and 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.
- Type
- article
- Published
- 2015-02-19
- Cited by
- 2,119
- References
- 12
- Access
- Open access
- OpenAlex
- https://openalex.org/W2128505445
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:18129003
Keywords
Computer science, MIT License, Software, File format, License
References
- Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics
- SAMBLASTER: fast duplicate marking and structural variant read extraction
- The D Programming Language
- Big data, but are we ready?
- 1000 Genomes Project
- The Sequence Alignment/Map format and SAMtools
- The Scramble conversion tool
- biobambam: tools for read pair collation based algorithms on BAM files
- Facing growth in the European Nucleotide Archive
- Parsing Computer Languages with an Automaton Compiled from a Single Regular Expression
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- Rethinking Data-Intensive Science Using Scalable Analytics Systems
- Super deduper, fast PCR duplicate detection in fastq files
- Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing
- High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome
- Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
- Mutated Huntingtin Causes Testicular Pathology in Transgenic Minipig Boars
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
- Quantitative trait loci associated with natural diversity in water-use efficiency and response to soil drying in Brachypodium distachyon.
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- Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks
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- BAMQL: a query language for extracting reads from BAM files
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- Genomics of ovarian cancer progression reveals diverse metastatic trajectories including intraepithelial metastasis to the fallopian tube
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