颜林林
(2022-08-01 01:02):
#paper doi:10.1093/bioinformatics/btac528 Bioinformatics, 2022, The K-mer File Format: a standardized and compact disk representation of sets of k-mers. 由k个字符连在一起的短串，称为k-mer，在生信的许多工具或分析过程中，如构建de Bruijn图（进行基因组组装）和创建序列索引（进行短序列比对），基本都会用到这个概念，并统计每种k-mer的出现频次，以及其他相关信息（如出现在基因组中的位置、与其他k-mer之间的关系）。随着k的增加，k-mer的种类呈几何数量增长，这给计算、存储都带来巨大开销。为此，本文开发了一种文件存储格式，用于存储k-mer信息，确保信息得以压缩存储的同时，还能保持高效的读写。说实话，这活不复杂，会点儿C++和Rust就能做，而且类似需求也不少。
The K-mer File Format: a standardized and compact disk representation of sets of k-mers
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Abstract:
SUMMARY: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3-5× compared to other formats, and bringing interoperability across tools.AVAILABILITY AND IMPLEMENTATION: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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