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

Motivation Despite constantly improving methods of genome sequencing, the task of error-free eukaryotic genome assembly is not yet solved. Among other kinds of problems of eukaryotic genome assembly are so-called “haplotypic duplications”, which may manifest themselves as cases when alleles are mistakenly assembled as paralogs. Haplotypic duplications are dangerous as they create illusions of gene family expansions and, thus, may bring a scientist to wrong conclusions about genome evolution and functioning. Results Here, I present Mabs, a suite of tools that serve as parameter optimizers of popular genome assemblers Hifiasm and Flye. By optimizing parameters of Hifiasm and Flye, Mabs tries to create assemblies where genes are 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 Hifiasm and Flye did when they were run with default parameters. When assemblies of Mabs, Hifiasm and Flye were postprocessed by a popular tool for haplotypic duplications removal Purge_dups, genes were better assembled by Mabs in 5 out of 6 cases. Availability and implementation Mabs has been written in Python and is available at https://github.com/shelkmike/Mabs