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Mabs, a suite of tools for gene-informed genome assembly

BACKGROUND: Despite 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...

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Autor principal: Schelkunov, Mikhail I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548655/
https://www.ncbi.nlm.nih.gov/pubmed/37794322
http://dx.doi.org/10.1186/s12859-023-05499-3
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author Schelkunov, Mikhail I.
author_facet Schelkunov, Mikhail I.
author_sort Schelkunov, Mikhail I.
collection PubMed
description BACKGROUND: Despite 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. RESULTS: Here, 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. CONCLUSIONS: Mabs is useful for making high-quality genome assemblies. It is available at https://github.com/shelkmike/Mabs SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05499-3.
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spelling pubmed-105486552023-10-05 Mabs, a suite of tools for gene-informed genome assembly Schelkunov, Mikhail I. BMC Bioinformatics Software BACKGROUND: Despite 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. RESULTS: Here, 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. CONCLUSIONS: Mabs is useful for making high-quality genome assemblies. It is available at https://github.com/shelkmike/Mabs SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05499-3. BioMed Central 2023-10-04 /pmc/articles/PMC10548655/ /pubmed/37794322 http://dx.doi.org/10.1186/s12859-023-05499-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Schelkunov, Mikhail I.
Mabs, a suite of tools for gene-informed genome assembly
title Mabs, a suite of tools for gene-informed genome assembly
title_full Mabs, a suite of tools for gene-informed genome assembly
title_fullStr Mabs, a suite of tools for gene-informed genome assembly
title_full_unstemmed Mabs, a suite of tools for gene-informed genome assembly
title_short Mabs, a suite of tools for gene-informed genome assembly
title_sort mabs, a suite of tools for gene-informed genome assembly
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548655/
https://www.ncbi.nlm.nih.gov/pubmed/37794322
http://dx.doi.org/10.1186/s12859-023-05499-3
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