The complete genome of <i>Escherichia coli</i> JM101 assembled with a combination of Nanopore and Illumina platforms

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ABSTRACT

We report the complete genome and the plasmid (F′ episome) sequences of Escherichia coli JM101 assembled with a combination of Nanopore and Illumina data. The resulting genome is a single contig of 4,524,963 bp, and the plasmid consists of a single contig of 197,186 bp.

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Bruce Walker, Thomas Abeel, Terrance Shea … (2014)

Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.

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QUAST: quality assessment tool for genome assemblies.

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi … (2013)

Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. http://bioinf.spbau.ru/quast . Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Fernando Astudillo: Role: Data curationRole: Formal analysisRole: MethodologyRole: SoftwareRole: Supervision

Violeta Larios: Role: Data curationRole: Formal analysisRole: Software

Noemí Flores: Role: ConceptualizationRole: ResourcesRole: ValidationRole: Writing – original draftRole: Writing – review and editing

Guillermo Gosset: Role: ConceptualizationRole: SupervisionRole: Writing – original draftRole: Writing – review and editing

Francisco Bolívar: Role: ConceptualizationRole: Funding acquisitionRole: ResourcesRole: Writing – original draftRole: Writing – review and editing

Matthew Champion: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (publisher-id): mra

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic, collection): February 2024

Publication date (Electronic, pub): 16 January 2024

Publication date PMC-release: 16 January 2024

Volume: 13

Issue: 2

Electronic Location Identifier: e00973-23

Affiliations

[1 ]Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México; , Cuernavaca, Morelos, México

[2 ]Winter Genomics, Salavery; , Ciudad de México, México

University of Notre Dame; , USA

Author notes

Address correspondence to Francisco Bolívar, francisco.bolivar@ 123456ibt.unam.mx

The authors declare no conflict of interest.

Author information

Adelfo Escalante https://orcid.org/0000-0002-5895-3694

Article

Publisher ID: 00973-23 Publisher ID: MRA.00973-23

DOI: 10.1128/MRA.00973-23

PMC ID: 10868158

PubMed ID: 38226818

SO-VID: de233697-9dda-4b96-a390-0d2a33b2686f

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 12 October 2023

Date accepted : 15 December 2023

Page count

supplementary-material: 0, authors: 6, Tables: 1, References: 10, Pages: 3, Words: 1233

Funding

Funded by: PAPIIT UNAM;

Award ID: IN209421

Award Recipient : Francisco Bolívar

Custom metadata

cover-date February 2024

Keywords: escherichia coli jm101,complete genome,f′ episome,nanopore,illumina

Data availability:

Keywords: escherichia coli jm101, complete genome, f′ episome, nanopore, illumina

The complete genome of Escherichia coli JM101 assembled with a combination of Nanopore and Illumina platforms

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ABSTRACT

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Genome Integrity

Most cited references 10

Trimmomatic: a flexible trimmer for Illumina sequence data

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

QUAST: quality assessment tool for genome assemblies.

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