Scientific Reports (May 2017)

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

  • Fanny-Dhelia Pajuste,
  • Lauris Kaplinski,
  • Märt Möls,
  • Tarmo Puurand,
  • Maarja Lepamets,
  • Maido Remm

DOI
https://doi.org/10.1038/s41598-017-02487-5
Journal volume & issue
Vol. 7, no. 1
pp. 1 – 10

Abstract

Read online

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” 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/).