Megadepth：BigWigs 和 BAMs 的高效覆盖度量化。
Megadepth: efficient coverage quantification for BigWigs and BAMs.
机构信息
Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Molecular Neuroscience Institute of Neurology, University College London (UCL), London WC1E 6BT, UK.
出版信息
Bioinformatics. 2021 Sep 29;37(18):3014-3016. doi: 10.1093/bioinformatics/btab152.
MOTIVATION
A common way to summarize sequencing datasets is to quantify data lying within genes or other genomic intervals. This can be slow and can require different tools for different input file types.
RESULTS
Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files, using substantially less memory than the next-fastest competitor. Megadepth can summarize coverage within all disjoint intervals of the Gencode V35 gene annotation for more than 19 000 GTExV8 BigWig files in approximately 1 h using 32 threads. Megadepth is available both as a command-line tool and as an R/Bioconductor package providing much faster quantification compared to the rtracklayer package.
AVAILABILITY AND IMPLEMENTATION
https://github.com/ChristopherWilks/megadepth, https://bioconductor.org/packages/megadepth.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
总结测序数据集的一种常见方法是量化基因或其他基因组区间内的数据。这可能很慢，并且对于不同的输入文件类型可能需要不同的工具。
结果
Megadepth 是一种快速的工具，可用于量化 BigWig 和 BAM/CRAM 输入文件的比对和覆盖度，使用的内存比下一个最快的竞争对手少得多。使用 32 个线程，Megadepth 可以在大约 1 小时内对超过 19000 个 GTExV8 BigWig 文件的 Gencode V35 基因注释的所有不相交区间内的覆盖度进行汇总。Megadepth 既可以作为命令行工具使用，也可以作为 R/Bioconductor 包使用，与 rtracklayer 包相比，它提供了更快的量化速度。
可用性和实现
https://github.com/ChristopherWilks/megadepth，https://bioconductor.org/packages/megadepth。
补充信息
补充数据可在 Bioinformatics 在线获得。
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