Medical Sciences Department, University of Turin, 10126 Turin, Italy.
Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK.
Bioinformatics. 2022 Apr 28;38(9):2617-2618. doi: 10.1093/bioinformatics/btac125.
Many genomics applications require the computation of nucleotide coverage of a reference genome or the ability to determine how many reads map to a reference region.
BamToCov is a toolkit for rapid and flexible coverage computation that relies on the most memory efficient algorithm and is designed for integration in pipelines, given its ability to read alignment files from streams. The tools in the suite can process sorted BAM or CRAM files, allowing the user to extract coverage information via different filtering approaches and to save the output in different formats (BED, Wig or counts). The BamToCov algorithm can also handle strand-specific and/or physical coverage analyses.
This program, accessory utilities and their documentation are freely available at https://github.com/telatin/BamToCov.
Supplementary data are available at Bioinformatics online.
许多基因组学应用都需要计算参考基因组的核苷酸覆盖度，或者确定有多少reads 映射到参考区域。
BamToCov 是一个快速、灵活的覆盖度计算工具包，它依赖于最节省内存的算法，并设计用于集成到管道中，因为它能够从流中读取对齐文件。该套件中的工具可以处理排序的 BAM 或 CRAM 文件，允许用户通过不同的过滤方法提取覆盖信息，并以不同的格式（BED、Wig 或计数）保存输出。BamToCov 算法还可以处理链特异性和/或物理覆盖度分析。
这个程序、附属实用程序及其文档可在 https://github.com/telatin/BamToCov 上免费获得。
补充数据可在 Bioinformatics 在线获得。
