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

Bioinformatics (Oxford, England) Pub Date : 2025-05-06 DOI:10.1093/bioinformatics/btaf175

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

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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).

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科罗拉多：一个完整的染色体尺度从头基因组组装的蛇尾工作流程。

动机：从头组装创造了参考基因组，为许多现代生物多样性和保护研究奠定了基础。世界各地的实验室正在组装大量新的基因组。为了避免重复的工作和可变的数据质量，我们需要一个最佳实践的组装过程，实现为一个自动化的可移植工作流。结果：在这里，我们展示了Colora，这是一种使用Pacific Biosciences HiFi， Hi-C和可选的Oxford Nanopore Technologies reads作为输入的snakmakake工作流程，可以产生染色体尺度的全新初级或分阶段基因组组装，并完成细胞器。Colora是一种用户友好的、多功能的、可重复的管道，可供研究人员寻找一种自动化的方法来获得高质量的从头开始的基因组组装。可用性和实现：Colora的源代码可在GitHub （https://github.com/LiaOb21/colora）上获得，并已存放在Zenodo的DOI https://doi.org/10.5281/zenodo.13321576下。Colora也可以在Snakemake工作流目录(https://snakemake.github.io/snakemake-workflow-catalog/？使用= LiaOb21 % 2 fcolora)。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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