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

Lia Obinu; Timothy Booth; Heleen De Weerd; Urmi Trivedi; Andrea Porceddu

doi:10.1093/bioinformatics/btaf175

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

Lia Obinu^*, Timothy Booth, Heleen De Weerd, Urmi Trivedi, Andrea Porceddu

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

MOTIVATION: 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.

RESULTS: 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.

AVAILABILITY AND IMPLEMENTATION: 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).

Original language	English
Article number	btaf175
Number of pages	11
Journal	Bioinformatics
Volume	41
Issue number	5
Early online date	16 Apr 2025
DOIs	https://doi.org/10.1093/bioinformatics/btaf175
Publication status	Published - May 2025

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10.1093/bioinformatics/btaf175Licence: Creative Commons: Attribution (CC-BY)

btaf175Final published version, 4.74 MBLicence: Creative Commons: Attribution (CC-BY)

1 Software

LiaOb21/colora: v_1.1.0 - Aghina
Obinu, L. & Booth, T., 14 Aug 2025
Research output: Non-textual form › Software

Open Access

Cite this

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title = "Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly",

abstract = "MOTIVATION: 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.RESULTS: 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.AVAILABILITY AND IMPLEMENTATION: 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).",

author = "Lia Obinu and Timothy Booth and \{De Weerd\}, Heleen and Urmi Trivedi and Andrea Porceddu",

note = "The authors would like to thank the organizers of Biodiversity Genomics Academy 2023 (https://bga23.org/), which was essential for acquiring the knowledge that determined the success of this project.",

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AU - Booth, Timothy

AU - De Weerd, Heleen

AU - Trivedi, Urmi

AU - Porceddu, Andrea

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ER -

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

Abstract

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Research output

LiaOb21/colora: v_1.1.0 - Aghina

Cite this