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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.*

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

Genome Biol. 20:284 (2019)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Rust Resistance Genes; Wheat; Progenitor; Alignment; Rna; Annotation; Diversity; Database; Program
ISSN (print) / ISBN 1474-760X
e-ISSN 1465-6906
Journal Genome Biology
Quellenangaben Volume: 20, Issue: 1, Pages: , Article Number: 284 Supplement: ,
Publisher BioMed Central
Publishing Place Campus, 4 Crinan St, London N1 9xw, England
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)