Source Code for Biology and Medicine | |
Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments | |
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 |
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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.
【 预 览 】
Files | Size | Format | View |
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20140709072113704.pdf | 339KB | download | |
Figure 1. | 49KB | Image | download |
【 图 表 】
Figure 1.
【 参考文献 】
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