ArticlePlant methods2022
A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes.
Article in Plant methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Unveiling centromeric retrotransposon dynamics through a high-quality rye genome assembly.Nature communications · 2026Article
- Extensive variation between chromosomes of North American and European hop.Nature communications · 2026Article
- A pangenome and pantranscriptome of hexaploid oat.Nature · 2026Article
- Article
- Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra.Scientific reports · 2025Article
- An annotated haplotype-resolved genome sequence assembly of diploid German chamomile, Matricaria chamomilla.Scientific data · 2025Article
- Article
- A single NLR gene confers resistance to leaf and stripe rust in wheat.Nature communications · 2024Article
- Are cereal grasses a single genetic system?Nature plants · 2024Article
- quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.Horticulture research · 2023Article
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4 authors.
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Abstract
backgroundAs 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.
resultsWe 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.
conclusionEven 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 .
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