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

Abstract

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

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

“…1l ). High accurately assembled genes (AG) scores were also obtained by Mabs 25 with consistent sequencing coverage for single- and multicopy genes (Extended Data Fig. 1n and Supplementary Fig.…”

“…Second, assembly contiguity was assessed by LTR Assembly Index (LAI) 23 following the standard of Draft: 0 ≤ LAI < 10, Reference: 10 ≤ LAI < 20, and Gold: 20 ≤ LAI. We further used calculate_AG in Mabs (v2.19) 25 (–local_busco_dataset Poales_odb10) to determine the count of accurately assembled genes (AG). The AG values are calculated by summing the number of genes in both single- and true multicopy BUSCO orthogroups by distinguishing true from false ones based on sequencing coverage.…”

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole‐genome duplications

“…Oxford Nanopore reads were trimmed by Porechop (Wick, n.d.). The genome of H. sosnowskyi was assembled by Mabs‐hifiasm (Schelkunov, 2023), Hifiasm (Cheng et al., 2021), Flye (Kolmogorov et al., 2019), Miniasm (Li, 2016), and Canu (Nurk et al., 2020). After assembly, haplotypic duplication removal was performed by Purge_dups (Guan et al., 2020).…”

“…After assembly, haplotypic duplication removal was performed by Purge_dups (Guan et al., 2020). To compare the gene assembly quality in these assemblies, BUSCO (Simão et al., 2015) and calculate_AG (Schelkunov, 2023) were used. The assembly with the most accurately assembled genes was the assembly made by Mabs without Purge_dups; this assembly was used in further analyses.…”

“…We found that Hifiasm performed better than other assemblers; however, it produced many duplicated genes due to incomplete collapsing of haplotypes. To overcome this problem, we used the tool Mabs-an add-on to long-read assemblers that allows automatic optimization of assembly parameters (Schelkunov, 2023). The application of Mabs improved the assembly both in terms of N50 and a fraction of duplicate genes (Table 1, Table S2).…”