MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment

作者：Dirk‐Jan M. van Workum, Kuntal Kumar Dey, Alexander Kozik, Dean Lavelle, Dick de Ridder, M Eric Schranz, Richard W Michelmore, Sandra Smit · 发表于：NAR Genomics and Bioinformatics · 年份：2026 · DOI：10.1093/nargab/lqag008 · 被引用次数：1 · 研究领域：Genomics and Phylogenetic Studies、Genomics and Rare Diseases、Genome Rearrangement Algorithms

With the current speed of sequencing, there is a desire for standardized and automated genome assembly and annotation to produce high-quality genomes as input for comparative (pan)genomics. Therefore, we created a convenience pipeline using existing tools that creates annotated genome assemblies from HiFi (and optionally ultra-long ONT and/or Hi-C) reads for a set of related individuals as well as a related reference genome. Our pipeline is species-agnostic and generates an extensive quality assessment report that can be used for manual filtering and refinement of the assembly and annotation. It includes statistics for individual completeness and contamination assessments as well as a concise pangenome view. The pipeline is implemented in Snakemake and available with a GPLv3 licence at GitHub under github.com/dirkjanvw/MoGAAAP, at Zenodo under doi.org/10.5281/zenodo.14833021, and can be installed through Bioconda.