LNISKS: Reference-free mutation identification for large and complex crop genomes

Nathan S. Watson-Haigh; Radoséphane Deschamps; Victor Llaca; Petra Wolters; Nathan S. Watson-Haigh; Margaret Pallotta; Ryan Whitford; Ute Baumann

doi:10.1101/580829

LNISKS: Reference-free mutation identification for large and complex crop genomes

Nathan S. Watson-Haigh, Radoséphane Deschamps, Victor Llaca, Petra Wolters, Nathan S. Watson-Haigh, Margaret Pallotta, Ryan Whitford, Ute Baumann

Research output: Other contribution › peer-review

Abstract

Mutation discovery is often key to the identification of genes responsible for major phenotypic traits.
In the context of bulked segregant analysis, common reference-based computational approaches are not
always suitable as they rely on a genome assembly which may be incomplete or highly divergent from
the studied accession. Reference-free methods based on short sequences of length k (k-mers), such as
NIKS, exploit redundancy of information across pools of recombinant genomes. Building on concepts
from NIKS we introduce LNISKS, a mutation discovery method which is suited for large and repetitive
crop genomes. In our experiments, it rapidly and with high confidence, identified mutations from over
700 Gbp of bread wheat genomic sequence data. LNISKS is publicly available at https://github.com/
rsuchecki/LNISKS.

Original language	Undefined/Unknown
Number of pages	17
DOIs	https://doi.org/10.1101/580829
Publication status	Published or Issued - 19 Mar 2019

Keywords

Mutation
Crop
Genome
LNISKS

Access to Document

10.1101/580829

http://doi.org/10.1101/580829

Cite this

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title = "LNISKS: Reference-free mutation identification for large and complex crop genomes",

abstract = "Mutation discovery is often key to the identification of genes responsible for major phenotypic traits. In the context of bulked segregant analysis, common reference-based computational approaches are not always suitable as they rely on a genome assembly which may be incomplete or highly divergent from the studied accession. Reference-free methods based on short sequences of length k (k-mers), such as NIKS, exploit redundancy of information across pools of recombinant genomes. Building on concepts from NIKS we introduce LNISKS, a mutation discovery method which is suited for large and repetitive crop genomes. In our experiments, it rapidly and with high confidence, identified mutations from over 700 Gbp of bread wheat genomic sequence data. LNISKS is publicly available at https://github.com/ rsuchecki/LNISKS.",

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T1 - LNISKS: Reference-free mutation identification for large and complex crop genomes

AU - Watson-Haigh, Nathan S.

AU - Deschamps, Radoséphane

AU - Llaca, Victor

AU - Wolters, Petra

AU - Watson-Haigh, Nathan S.

AU - Pallotta, Margaret

AU - Whitford, Ryan

AU - Baumann, Ute

PY - 2019/3/19

Y1 - 2019/3/19

N2 - Mutation discovery is often key to the identification of genes responsible for major phenotypic traits. In the context of bulked segregant analysis, common reference-based computational approaches are not always suitable as they rely on a genome assembly which may be incomplete or highly divergent from the studied accession. Reference-free methods based on short sequences of length k (k-mers), such as NIKS, exploit redundancy of information across pools of recombinant genomes. Building on concepts from NIKS we introduce LNISKS, a mutation discovery method which is suited for large and repetitive crop genomes. In our experiments, it rapidly and with high confidence, identified mutations from over 700 Gbp of bread wheat genomic sequence data. LNISKS is publicly available at https://github.com/ rsuchecki/LNISKS.

AB - Mutation discovery is often key to the identification of genes responsible for major phenotypic traits. In the context of bulked segregant analysis, common reference-based computational approaches are not always suitable as they rely on a genome assembly which may be incomplete or highly divergent from the studied accession. Reference-free methods based on short sequences of length k (k-mers), such as NIKS, exploit redundancy of information across pools of recombinant genomes. Building on concepts from NIKS we introduce LNISKS, a mutation discovery method which is suited for large and repetitive crop genomes. In our experiments, it rapidly and with high confidence, identified mutations from over 700 Gbp of bread wheat genomic sequence data. LNISKS is publicly available at https://github.com/ rsuchecki/LNISKS.

KW - Mutation

KW - Crop

KW - Genome

KW - LNISKS

U2 - 10.1101/580829

DO - 10.1101/580829

M3 - Other contribution

ER -