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Updated: Apr 21, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

camlhmp: a simple framework for building reproducible microbial genome-based typing tools.

Robert A Petit^1,2, Chayse M Rowley¹, Taylor R Fearing¹

¹Wyoming Public Health Laboratory, Wyoming Department of Health, Cheyenne, Wyoming, USA.

Microbiology Resource Announcements

|April 20, 2026

Summary

This summary is machine-generated.

We created camlhmp, a framework to simplify microbial genomics typing tool development. This promotes consistency and community involvement in microbial sequence-based typing.

Keywords:

bioinformatics microbial genomics sequence-based typing software

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Last Updated: Apr 21, 2026

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Area of Science:

Microbial Genomics
Bioinformatics
Computational Biology

Background:

Sequence-based typing is crucial for understanding microbial populations.
Current typing tools are often developed independently, causing redundancy and format inconsistencies.
Limited community participation hinders the advancement of microbial typing methodologies.

Purpose of the Study:

To develop a unified framework for creating, executing, and maintaining microbial typing tools.
To address the challenges of duplicated effort and inconsistent formats in existing tools.
To foster greater community participation in the development of microbial genomics tools.

Main Methods:

Developed camlhmp, a novel framework for microbial typing tool development.
Utilized simple, human-readable YAML files for tool configuration and execution.
Provided a centralized platform accessible via GitHub (https://github.com/rpetit3/camlhmp).

Main Results:

camlhmp streamlines the creation and maintenance of sequence-based typing tools.
The framework promotes standardized formats and reduces duplicated efforts.
Facilitates easier execution and maintenance of typing tools.

Conclusions:

camlhmp offers a standardized and accessible solution for microbial typing tool development.
The framework is expected to enhance reproducibility and collaboration within the microbial genomics community.
Simplifying tool development can accelerate research in microbial genomics and epidemiology.