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

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

Posted 09 May 2019
bioRxiv DOI: 10.1101/631648 (published DOI: 10.1186/s13059-019-1899-5)

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 have developed 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 evaluated the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and constructed an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

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