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

Cécile Monat; Sudharsan Padmarasu; Thomas Lux; Thomas Wicker; Heidrun Gundlach; Axel Himmelbach; Jennifer Ens; Chengdao Li; Gary J. Muehlbauer; Alan H. Schulman; Robbie Waugh; Ilka Braumann; Curtis Pozniak; Uwe Scholz; Klaus F.X. Mayer; Manuel Spannagl; Nils Stein; Martin Mascher

doi:10.1186/s13059-019-1899-5

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

Cécile Monat, Sudharsan Padmarasu, Thomas Lux, Thomas Wicker, Heidrun Gundlach, Axel Himmelbach, Jennifer Ens, Chengdao Li, Gary J. Muehlbauer, Alan H. Schulman, Robbie Waugh, Ilka Braumann, Curtis Pozniak, Uwe Scholz, Klaus F.X. Mayer, Manuel Spannagl, Nils Stein, Martin Mascher

Agronomy and Plant Genetics

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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.

Original language	English (US)
Article number	284
Journal	Genome biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1899-5
State	Published - Dec 18 2019

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© 2019 The Author(s).

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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., & Mascher, M. (2019). TRITEX: Chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome biology, 20(1), Article 284. https://doi.org/10.1186/s13059-019-1899-5

Monat, C, Padmarasu, S, Lux, T, Wicker, T, Gundlach, H, Himmelbach, A, Ens, J, Li, C, Muehlbauer, GJ, Schulman, AH, Waugh, R, Braumann, I, Pozniak, C, Scholz, U, Mayer, KFX, Spannagl, M, Stein, N & Mascher, M 2019, 'TRITEX: Chromosome-scale sequence assembly of Triticeae genomes with open-source tools', Genome biology, vol. 20, no. 1, 284. https://doi.org/10.1186/s13059-019-1899-5

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

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