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bioRxiv · 10.1101/060822

FastGT: from raw sequence reads to 30 million genotypes in less than an hour

Fanny-Dhelia Pajuste·Lauris Kaplinski·Märt Möls·Tarmo Puurand·Maarja Lepamets·Maido Remm
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Abstract

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\" genomes1 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/).

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Fanny-Dhelia Pajuste, Lauris Kaplinski, Märt Möls, Tarmo Puurand, Maarja Lepamets, Maido Remm. 2016-06-28. FastGT: from raw sequence reads to 30 million genotypes in less than an hour. https://doi.org/10.1101/060822

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