CrossMap: a versatile tool for coordinate conversion between genome assemblies
CrossMap: a versatile tool for coordinate conversion between genome assemblies
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DOI：
10.1093/bioinformatics/btt730
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发表时间：
2014-04-01
期刊：
影响因子：
5.8
通讯作者：
Wang, Liguo
中科院分区：
文献类型：
--
作者：
Zhao, Hao;Sun, Zhifu;Wang, Liguo
动机：参考基因组组合不时会发生变化和改进。一般来说，研究人员需要将根据旧汇编分析的结果转换为新版本，反之亦然，以便于荟萃分析、直接比较、数据集成和可视化。几个有用的转换工具可以转换浏览器可扩展数据或通用特征格式的基因组间隔文件，但没有一个工具具有转换序列比对图或Bigwig格式文件的功能。这是计算基因组学工具中的一个重要缺口，因为这些格式是最广泛用于表示高通量测序数据的格式，如RNA-seq、染色质免疫沉淀测序、DNA-seq等。结果：我们开发了CrossMap，一个通用而高效的工具，用于在组装之间转换基因组坐标。CrossMap支持大多数常用的文件格式，包括BAM、序列比对图、Wigger、Bigwig、浏览器可扩展数据、通用特征格式、基因转移格式和变体调用格式。
Motivation: Reference genome assemblies are subject to change and refinement from time to time. Generally, researchers need to convert the results that have been analyzed according to old assemblies to newer versions, or vice versa, to facilitate meta-analysis, direct comparison, data integration and visualization. Several useful conversion tools can convert genome interval files in browser extensible data or general feature format, but none have the functionality to convert files in sequence alignment map or BigWig format. This is a significant gap in computational genomics tools, as these formats are the ones most widely used for representing high-throughput sequencing data, such as RNA-seq, chromatin immunoprecipitation sequencing, DNA-seq, etc.Results: Here we developed CrossMap, a versatile and efficient tool for converting genome coordinates between assemblies. CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensible data, general feature format, gene transfer format and variant call format.