A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes

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dc.contributor.authorMarone, Marina P.
dc.contributor.authorSingh, Harmeet C.
dc.contributor.authorPozniak, Curtis J.
dc.contributor.authorMascher, Martin
dc.date.accessioned2023-01-01T04:54:40Z
dc.date.issued2022-12-02
dc.date.updated2023-01-01T04:54:40Z
dc.description.abstractBackground As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects. Results We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive. Conclusion Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/ . The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly
dc.identifier.citationPlant Methods. 2022 Dec 02;18(1):128
dc.identifier.doi10.1186/s13007-022-00964-1
dc.identifier.urihttp://hdl.handle.net/1993/37039
dc.language.isoeng
dc.language.rfc3066en
dc.publisherBMC
dc.rightsopen accessen_US
dc.rights.holderThe Author(s)
dc.subjectGenome sequence assembly
dc.subjectChromosome conformation capture sequencing
dc.subjectLong-read sequence assembly
dc.subjectGenetic map
dc.subjectPangenome
dc.titleA technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes
dc.typeJournal Article
local.author.affiliationFaculty of Agricultural and Food Sciences::Department of Plant Science
oaire.citation.issue128
oaire.citation.titlePlant Methods
oaire.citation.volume18
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