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

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• High-throughput sequencing technologies necessitate standardized and automated methods for genome assembly and annotation.
• Producing high-quality genomes is crucial for downstream applications like comparative (pan)genomics.

Purpose of the Study:

• To develop a species-agnostic pipeline for automated, high-quality genome assembly and annotation.
• To integrate various sequencing data types (HiFi, ONT, Hi-C) for robust genome reconstruction.
• To provide comprehensive quality assessment reports for manual refinement and pangenome visualization.

Main Methods:

• Development of a Snakemake-based pipeline integrating existing bioinformatics tools.
• Input accommodates HiFi reads, with optional support for ultra-long ONT and Hi-C reads.
• Automated generation of quality assessment metrics including completeness, contamination, and pangenome overview.

Main Results:

• A species-agnostic pipeline, MoGAAAP, was successfully implemented for genome assembly and annotation.
• The pipeline produces extensive quality assessment reports, facilitating manual data refinement.
• It enables the generation of a concise pangenome view for related individuals and a reference genome.

Conclusions:

• The MoGAAAP pipeline offers a standardized and automated solution for generating high-quality annotated genomes.
• Its comprehensive quality control features support accurate genome assembly and annotation refinement.
• The pipeline is readily accessible via GitHub, Zenodo, and Bioconda for broad research community use.