RT Journal Article
SR Electronic
T1 LNISKS: Reference-free mutation identification for large and complex crop genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 580829
DO 10.1101/580829
A1 Radosław Suchecki
A1 Ajay Sandhu
A1 Stéphane Deschamps
A1 Victor Llaca
A1 Petra Wolters
A1 Nathan S. Watson-Haigh
A1 Margaret Pallotta
A1 Ryan Whitford
A1 Ute Baumann
YR 2019
UL http://biorxiv.org/content/early/2019/03/19/580829.abstract
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.