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

被引：29

作者：

Pajuste, Fanny-Dhelia ^{[1
]}

Kaplinski, Lauris ^{[1
]}

Mols, Mart ^{[1
,2
]}

Puurand, Tarmo ^{[1
]}

Lepamets, Maarja ^{[1
]}

Remm, Maido ^{[1
]}

机构：

[1] Univ Tartu, Inst Mol & Cell Biol, Tartu, Estonia

[2] Univ Tartu, Inst Math & Stat, Tartu, Estonia

来源：

SCIENTIFIC REPORTS | 2017年 / 7卷

关键词：

ERROR-CORRECTION; GENOME; DISCOVERY; PIPELINES; FRAMEWORK; TOOLKIT; SNP;

D O I：

10.1038/s41598-017-02487-5

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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/).

引用

页数：10

共 17 条

[1] 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
Scientific Reports, 7
[2] KmerToCN: an alignment-free method for copy number estimation directly from next generation sequencing reads
Pajuste, Fanny-Dhelia
Remm, Maido
EUROPEAN JOURNAL OF HUMAN GENETICS, 2024, 32 : 672 - 672
[3] GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads
Pajuste, Fanny-Dhelia
Remm, Maido
SCIENTIFIC REPORTS, 2023, 13 (01)
[4] GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads
Fanny-Dhelia Pajuste
Maido Remm
Scientific Reports, 13
[5] Next generation sequencing reads comparison with an alignment-free distance
Weitschek E.
Santoni D.
Fiscon G.
De Cola M.C.
Bertolazzi P.
Felici G.
BMC Research Notes, 7 (1)
[6] Alignment-free method for gene copy number estimation from raw next generation sequencing data
Pajuste, Fanny-Dhelia
Remm, Maido
EUROPEAN JOURNAL OF HUMAN GENETICS, 2023, 31 : 604 - 604
[7] Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads
Song, Kai
Ren, Jie
Zhai, Zhiyuan
Liu, Xuemei
Deng, Minghua
Sun, Fengzhu
JOURNAL OF COMPUTATIONAL BIOLOGY, 2013, 20 (02) : 64 - 79
[8] A SIMPLE SHORTCUT TO UNSUPERVISED ALIGNMENT-FREE PHYLOGENETIC GENOME GROUPINGS, EVEN FROM UNASSEMBLED SEQUENCING READS
Maurer-Stroh, Sebastian
Gunalan, Vithiagaran
Wong, Wing-Cheong
Eisenhaber, Frank
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 2013, 11 (06)
[9] Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin
Raime, Kairi
Krjutskov, Kaarel
Remm, Maido
FRONTIERS IN PLANT SCIENCE, 2020, 11
[10] A Statistical Method for Alignment-Free Analysis of Sequencing Reads with Applications in Copy Number Determination and Plasmid Integration Detection
Mols, Mart
HUMAN HEREDITY, 2017, 83 (01) : 18 - 18

← 1 2 →