bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby
bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby
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DOI：
10.1093/bioinformatics/btv178
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发表时间：
2015-08-01
期刊：
影响因子：
5.8
通讯作者：
MacLean, Dan
中科院分区：
文献类型：
--
作者：
Etherington, Graham J.;Ramirez-Gonzalez, Ricardo H.;MacLean, Dan
动机：bio-samtools是SAMtools的一个Ruby语言接口，SAMtools是一个非常流行的库，它提供了用于以序列比对/映射格式操作高通量序列比对的实用程序。Ruby的进步，现在允许我们提高分析能力并增加bio-samtools实用程序，允许用户使用非常少量的代码完成大量的分析。bio-samtools也可以很容易地开发，包括额外的SAMtools方法，从而保持与最新的SAMtools版本。结果：我们为SAMtools发布的MPileup和变体调用格式（VCF）数据格式添加了新的Ruby类，并为变体分析引入了更多的分析方法，包括替代等位基因计算和SNP等位基因频率调用。我们新实现的bio-samtools还确保现在支持SAMtools库的所有功能，并且bio-samtools可以轻松扩展以包含SAMtools中的未来更改。Bio-SamTools 2还提供允许用户直接产生对准数据的可视化的方法。
Motivation: bio-samtools is a Ruby language interface to SAMtools, the highly popular library that provides utilities for manipulating high-throughput sequence alignments in the Sequence Alignment/Map format. Advances in Ruby, now allow us to improve the analysis capabilities and increase bio-samtools utility, allowing users to accomplish a large amount of analysis using a very small amount of code. bio-samtools can also be easily developed to include additional SAMtools methods and hence stay current with the latest SAMtools releases.Results: We have added new Ruby classes for the MPileup and Variant Call Format (VCF) data formats emitted by SAMtools and introduced more analysis methods for variant analysis, including alternative allele calculation and allele frequency calling for SNPs. Our new implementation of bio-samtools also ensures that all the functionality of the SAMtools library is now supported and that bio-samtools can be easily extended to include future changes in SAMtools. bio-samtools 2 also provides methods that allow the user to directly produce visualization of alignment data.