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 (Lead / Corresponding author), Martin Mascher (Lead / Corresponding author)

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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 languageEnglish
Article number284
Pages (from-to)1-18
Number of pages18
JournalGenome Biology
Volume20
Issue number1
DOIs
Publication statusPublished - 18 Dec 2019

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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), 1-18. [284]. https://doi.org/10.1186/s13059-019-1899-5