Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Assembling large genomes is complex and requires significant resources.
• There is a need for automated and reproducible workflows for genome assembly.

Purpose of the Study:

• To present Pipeasm, an automated genome assembly pipeline.
• To streamline the process of creating high-quality chromosome-scale genome assemblies.

Main Methods:

• Pipeasm utilizes Snakemake and Singularity for containerized workflow management.
• The pipeline integrates various data types, including HiFi, ONT, and Hi-C reads.
• Automated steps include read trimming, nuclear and mitogenome assembly, scaffolding, decontamination, and quality evaluation.

Main Results:

• Pipeasm generated high-quality genome assemblies for four vertebrate species.
• Assemblies exhibited scaffold L50 proportional to genome size and up to 99.6% BUSCO completeness.
• The pipeline provides detailed reports, genome statistics, and Hi-C maps.

Conclusions:

• Pipeasm offers an efficient, reproducible, and automated solution for genome assembly.
• The pipeline is adaptable and supports future updates to assembly standards.
• Pipeasm facilitates the generation of high-quality genome assemblies for diverse species.