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

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

doi:10.1186/s13059-019-1899-5

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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, 284. https://doi.org/10.1186/s13059-019-1899-5

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 o