Etherington Graham J, Ramirez-Gonzalez Ricardo H, MacLean Dan
The Sainsbury Laboratory and.
The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK.
Bioinformatics. 2015 Aug 1;31(15):2565-7. doi: 10.1093/bioinformatics/btv178. Epub 2015 Mar 29.
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.
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.
bio - samtools是一个用于SAMtools的Ruby语言接口，SAMtools是一个非常流行的库，提供了用于处理序列比对/映射（Sequence Alignment/Map）格式的高通量序列比对的实用工具。Ruby语言的发展，现在使我们能够提高分析能力并增加bio - samtools的实用性，允许用户使用非常少量的代码完成大量分析。bio - samtools也可以很容易地进行开发，以包含额外的SAMtools方法，从而跟上SAMtools的最新版本。
我们为SAMtools发出的MPileup和变异调用格式（VCF）数据格式添加了新的Ruby类，并引入了更多用于变异分析的方法，包括单核苷酸多态性（SNP）的替代等位基因计算和等位基因频率调用。我们新的bio - samtools实现还确保现在支持SAMtools库的所有功能，并且bio - samtools可以很容易地扩展以包含SAMtools未来的变化。bio - samtools 2还提供了允许用户直接生成比对数据可视化的方法。
