FastGT：一种从原始测序读段中直接调用常见单核苷酸变异（SNVs）的无需比对方法。
FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads.
机构信息
Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia.
出版信息
Sci Rep. 2017 May 31;7(1):2537. doi: 10.1038/s41598-017-02487-5.
We have developed a computational method that counts the frequencies of unique k-mers in FASTQ-formatted genome data and uses this information to infer the genotypes of known variants. FastGT can detect the variants in a 30x genome in less than 1 hour using ordinary low-cost server hardware. The overall concordance with the genotypes of two Illumina "Platinum" genomes is 99.96%, and the concordance with the genotypes of the Illumina HumanOmniExpress is 99.82%. Our method provides k-mer database that can be used for the simultaneous genotyping of approximately 30 million single nucleotide variants (SNVs), including >23,000 SNVs from Y chromosome. The source code of FastGT software is available at GitHub (https://github.com/bioinfo-ut/GenomeTester4/).
我们开发了一种计算方法，可对 FASTQ 格式的基因组数据中的独特 k-mer 进行计数，并利用这些信息推断已知变体的基因型。FastGT 可以在不到 1 小时的时间内使用普通的低成本服务器硬件检测 30x 基因组中的变体。与两个 Illumina“Platinum”基因组的基因型总体一致性为 99.96%，与 Illumina HumanOmniExpress 的基因型一致性为 99.82%。我们的方法提供了 k-mer 数据库，可用于对大约 3000 万个单核苷酸变体 (SNV) 进行同时基因分型，包括来自 Y 染色体的 >23,000 个 SNV。FastGT 软件的源代码可在 GitHub 上获得（https://github.com/bioinfo-ut/GenomeTester4/）。
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