Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-12

AUTHORS

Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo, Daniel MacLean

ABSTRACT

BACKGROUND: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities are implemented in C and provide an API for programmatic access, to help make this functionality available to programmers wishing to develop in the high level Ruby language we have developed bio-samtools, a Ruby binding to the SAMtools library. RESULTS: The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned. CONCLUSIONS: Bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format. More... »

PAGES

6

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1751-0473-7-6

DOI

http://dx.doi.org/10.1186/1751-0473-7-6

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1015634713

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22640879


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