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

## TL;DR

MoGAAAP is a pipeline that automates genome assembly and annotation using various sequencing data, providing quality assessments for comparative genomics.

## Contribution

The novelty lies in a modular, automated pipeline for genome assembly and annotation with comprehensive quality assessment.

## Key findings

- The pipeline is species-agnostic and supports HiFi, ONT, and Hi-C reads.
- It generates detailed quality reports for assembly and annotation.
- The pipeline is implemented in Snakemake and is publicly available for use.

## Abstract

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.