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TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Monat, C., Padmarasu, S., Lux, T., Wicker, T., Gundlach, H., Himmelbach, A., Ens, J., Li, C., Muehlbauer, G.J., Schulman, A.H., Waugh, R., Braumann, I., Pozniak, C., Scholz, U., Mayer, K.F.X., Spannagl, M., Stein, N. and Mascher, M. (2019) TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biology, 20 (1).

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Abstract

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.

Item Type: Journal Article
Murdoch Affiliation: Western Barley Genetics Alliance
School of Veterinary and Life Sciences
Publisher: BioMed Central
Copyright: © 2019 The Author(s).
URI: http://researchrepository.murdoch.edu.au/id/eprint/54059
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