文章基本信息

标题：Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
本地全文：下载
作者：Ricardo H Ramirez-Gonzalez ; Raoul Bonnal ; Mario Caccamo 等
期刊名称：Source Code for Biology and Medicine
印刷版ISSN：1751-0473
电子版ISSN：1751-0473
出版年度：2012
卷号：7
期号：1
页码：6
DOI：10.1186/1751-0473-7-6
语种：English
出版社：BioMed Central
摘要：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. 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. 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.
关键词：Next-generation sequencing ; DNA ; High ; Throughput ; Ruby ; Bio ; SAM ; BAM