Preprint
LNISKS: Reference-free mutation identification for large and complex crop genomes
bioRxiv : the preprint server for biology
Cold Spring Harbor Laboratory
2019
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.
Details
- Title
- LNISKS: Reference-free mutation identification for large and complex crop genomes
- Authors/Creators
- Radoslaw SucheckiAjay Sandhu - Pioneer Hi-BredStephane DeschampsVictor Llaca - Corteva (United States)Petra Wolters - Pioneer Hi-BredNathan S Watson-Haigh - Australian Centre for Plant Functional GenomicsMargaret Pallotta - The University of AdelaideRyan Whitford - Murdoch University, Centre for Crop and Food InnovationUte Baumann - The University of Adelaide
- Publication Details
- bioRxiv : the preprint server for biology
- Publisher
- Cold Spring Harbor Laboratory
- Identifiers
- 991005796267207891
- Copyright
- The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
- Murdoch Affiliation
- Centre for Crop and Food Innovation
- Resource Type
- Preprint
Metrics
7 Record Views