CRAM 3.1：CRAM 文件格式的新进展。

CRAM 3.1: advances in the CRAM file format.

机构信息

Informatics and Digital Solutions, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.

出版信息

Bioinformatics. 2022 Mar 4;38(6):1497-1503. doi: 10.1093/bioinformatics/btac010.

DOI:10.1093/bioinformatics/btac010

PMID:34999766

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8896640/

Abstract

MOTIVATION

CRAM has established itself as a high compression alternative to the BAM file format for DNA sequencing data. We describe updates to further improve this on modern sequencing instruments.

RESULTS

With Illumina data CRAM 3.1 is 7-15% smaller than the equivalent CRAM 3.0 file, and 50-70% smaller than the corresponding BAM file. Long-read technology shows more modest compression due to the presence of high-entropy signals.

AVAILABILITY AND IMPLEMENTATION

The CRAM 3.0 specification is freely available from https://samtools.github.io/hts-specs/CRAMv3.pdf. The CRAM 3.1 improvements are available in a separate OpenSource HTScodecs library from https://github.com/samtools/htscodecs, and have been incorporated into HTSlib.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

CRAM 已经成为 DNA 测序数据的 BAM 文件格式的一种高效压缩替代方案。我们描述了进一步改进现代测序仪器上这种方案的更新。

结果

对于 Illumina 数据，CRAM 3.1 比等效的 CRAM 3.0 文件小 7-15%，比相应的 BAM 文件小 50-70%。由于存在高熵信号，长读技术的压缩效果要适度一些。

可用性和实现

CRAM 3.0 规范可从 https://samtools.github.io/hts-specs/CRAMv3.pdf 免费获得。CRAM 3.1 的改进可从 https://github.com/samtools/htscodecs 的单独开源 HTScodecs 库获得，并已被纳入 HTSlib。