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

Source Code for Biology and Medicine

Daniel MacLean¹  Mario Caccamo²  Raoul Bonnal³  Ricardo H Ramirez-Gonzalez² 

[1] The Sainsbury Laboratory, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK;The Genome Analysis Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK;Istituto Nazionale Genetica Molecolare, Via F. Sforza 28, Milan 20122, Italy

关键词: BAM;    SAM;    Bio;    Ruby;    Throughput;    High;    DNA;    Next-generation sequencing;   

Others  :  811756
DOI  :  10.1186/1751-0473-7-6

 received in 2012-04-26, accepted in 2012-04-26,  发布年份 2012

【 摘 要 】

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.

【 授权许可】

   
2012 Ramirez-Gonzalez et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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