ArticleBMC bioinformatics2023
Mabs, a suite of tools for gene-informed genome assembly.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A Chromosome-Scale Genome Assembly and Annotation of the Antarctic Pearlwort Colobanthus quitensis (Caryophyllaceae).Genome biology and evolution · 2026Article
- A phased, near-telomere-to-telomere chromosome-scale reference genome of the Moroccan argan tree.Scientific data · 2026Article
- Chromosome-level genome assembly of the Vermilion Snapper (Rhomboplites aurorubens).Scientific data · 2025Article
- Comparative Genomics Reveals Ancient and Unique Pathogenicity Features in AustralianJournal of fungi (Basel, Switzerland) · 2025Article
- Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-Scale Assembly of Capsella orientalis, Maternal Progenitor of Cosmopolitan Allotetraploid C. bursa-pastoris.Genome biology and evolution · 2025Article
- Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance.Nature genetics · 2024Article
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Authors and funding
1 author.
Funding
Abstract
backgroundDespite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds of problems of eukaryotic genome assembly are so-called "haplotypic duplications", which may manifest themselves as cases of alleles being mistakenly assembled as paralogues. Haplotypic duplications are dangerous because they create illusions of gene family expansions and, thus, may lead scientists to incorrect conclusions about genome evolution and functioning.
resultsHere, I present Mabs, a suite of tools that serve as parameter optimizers of the popular genome assemblers Hifiasm and Flye. By optimizing the parameters of Hifiasm and Flye, Mabs tries to create genome assemblies with the genes assembled as accurately as possible. Tests on 6 eukaryotic genomes showed that in 6 out of 6 cases, Mabs created assemblies with more accurately assembled genes than those generated by Hifiasm and Flye when they were run with default parameters. When assemblies of Mabs, Hifiasm and Flye were postprocessed by a popular tool for haplotypic duplication removal, Purge_dups, genes were better assembled by Mabs in 5 out of 6 cases.
conclusionsMabs is useful for making high-quality genome assemblies. It is available at https://github.com/shelkmike/Mabs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.