TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools.
- Monat C Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Padmarasu S Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Lux T PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.
- Wicker T Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
- Gundlach H PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.
- Himmelbach A Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Ens J Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada.
- Li C Western Barley Genetics Alliance, School of Veterinary and Life Sciences (VLS), Murdoch University, Murdoch, WA, Australia.
- Muehlbauer GJ Department of Agronomy and Plant Genetics & Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA.
- Schulman AH Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- Waugh R The James Hutton Institute, Dundee, UK.
- Braumann I Carlsberg Research Laboratory, Copenhagen, Denmark.
- Pozniak C Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada.
- Scholz U Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Mayer KFX PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.
- Spannagl M PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.
- Stein N Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. stein@ipk-gatersleben.de.
- Mascher M Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. mascher@ipk-gatersleben.de.
- 2019-12-19
Published in:
- Genome biology. - 2019
English
Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
- Language
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- English
- Open access status
- gold
- Identifiers
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- DOI 10.1186/s13059-019-1899-5
- PMID 31849336
- Persistent URL
- https://folia.unifr.ch/global/documents/135050
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