Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 40238183.
- Also identified by DOI 10.1093/bioinformatics/btaf175 and PMC identifier 12065627.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
De novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow. Here, we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using Pacific Biosciences HiFi, Hi-C, and optionally Oxford Nanopore Technologies reads as input. Colora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies. The source code of Colora is available on GitHub (https://github.com/LiaOb21/colora) and has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora).
Medical subject headings
- Software
- Genomics
- Chromosomes
- Genome