Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• De novo genome assembly is crucial for biodiversity and conservation research, with numerous labs worldwide generating new reference genomes.
• A standardized, automated workflow is needed to ensure consistent data quality and prevent duplicated efforts in genome assembly.

Purpose of the Study:

• To present Colora, an automated, portable workflow for de novo genome assembly.
• To provide researchers with a user-friendly and reproducible pipeline for generating high-quality genome assemblies.

Main Methods:

• Developed Colora as a Snakemake workflow.
• Designed to process Pacific Biosciences HiFi, Hi-C, and Oxford Nanopore Technologies sequencing reads.
• Enables the production of chromosome-scale primary or phased genome assemblies, including organelles.

Main Results:

• Introduced Colora, a versatile and reproducible de novo genome assembly pipeline.
• The workflow successfully generates chromosome-scale assemblies with organelle genomes.
• Colora is user-friendly and ready for implementation in research settings.

Conclusions:

• Colora offers a best-practice, automated solution for de novo genome assembly.
• The workflow enhances reproducibility and data quality in genomics studies.
• Facilitates efficient genome assembly for biodiversity and conservation efforts.