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Updated: Mar 1, 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

Millstone: software for multiplex microbial genome analysis and engineering.

Daniel B Goodman^1,2, Gleb Kuznetsov^1,2,3, Marc J Lajoie^1,2

¹Department of Genetics, Harvard Medical School, Boston, MA, USA.

|May 27, 2017

Summary

This summary is machine-generated.

Millstone is a new web platform that automates computational analysis for microbial genome engineering and adaptive laboratory evolution. It simplifies genotype comparison and genome design for large-scale projects.

Keywords:

Bioinformatics Experimental evolution Genome engineering Laboratory evolution Microbial evolution Synthetic biology Synthetic genomics Whole-genome sequencing

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Published on: August 20, 2021

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Published on: June 28, 2018

Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

Advances in DNA sequencing and genome editing technologies have accelerated microbial research.
Computational analysis of large genomic datasets has become a bottleneck in adaptive laboratory evolution and microbial genome engineering.

Purpose of the Study:

To introduce Millstone, a novel web-based platform designed to streamline computational analysis in microbial genome engineering.
To provide a scalable and accessible solution for genotype comparison and iterative genome design.

Main Methods:

Development of a web-based platform named Millstone.
Implementation of automated genotype comparison and visualization tools.
Integration of features for designing oligonucleotide libraries and creating successive reference genomes.

Main Results:

Millstone successfully automates genotype comparison for projects involving hundreds of genomic samples.
The platform facilitates iterative genome engineering by enabling the creation of updated reference genomes.
Millstone is open-source and deployable on various platforms, ensuring scalability.

Conclusions:

Millstone addresses the computational bottleneck in microbial genome engineering.
The platform offers a scalable, user-friendly solution for researchers in adaptive laboratory evolution and genome engineering.
Millstone's open-source nature promotes accessibility and adoption across different laboratory settings.