FastGT: an Alignment-free Method for Calling Common SNVs Directly from Raw Sequencing Reads

Overview

Journal Sci Rep

Specialty Science

Date 2017 Jun 2

PMID 28566690

Citations 22

Authors

Fanny-Dhelia Pajuste

Lauris Kaplinski

Mart Mols

Tarmo Puurand

Maarja Lepamets

Maido Remm

Affiliations

Soon will be listed here.

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/).

Citing Articles

Space-efficient computation of k-mer dictionaries for large values of k.

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SAKE: Strobemer-assisted k-mer extraction.

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GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads.

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DOCEST-fast and accurate estimator of human NGS sequencing depth and error rate.

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