Draft Genome Sequence of Plesiomonas shigelloides Strain PI-19, Isolated from the Intestine of Pufferfish (Tetraodon cutcutia)

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

ABSTRACT

We report the draft genome sequence of Plesiomonas shigelloides strain PI-19, which was isolated from the intestine of freshwater pufferfish. The genome of strain PI-19 contain 3,146 protein-coding sequences and harbors virulence genes associated with pathogenicity.

Related collections

Most cited references 12

Record: found
Abstract: found
Article: found

Is Open Access

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.

0 comments Cited 16564 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan Parks, Michael Imelfort, Connor Skennerton … (2015)

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

0 comments Cited 3003 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

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.

0 comments Cited 2883 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Subrata K. Das:

ORCID: https://orcid.org/0000-0002-7280-5751

David A. Baltrus: 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, pub): 2 March 2022

Publication date (Electronic, collection): March 2022

Publication date PMC-release: 2 March 2022

Volume: 11

Issue: 3

Electronic Location Identifier: e01252-21

Affiliations

[a ] Institute of Life Sciences, Department of Biotechnology, Bhubaneswar, India

[b ] Regional Center for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India

University of Arizona

Author notes

The authors declare no conflict of interest.

Author information

Subrata K. Das https://orcid.org/0000-0002-7280-5751

Article

Publisher ID: MRA01252-21 Publisher ID: mra.01252-21

DOI: 10.1128/mra.01252-21

PMC ID: 8928758

PubMed ID: 35234506

SO-VID: b8db9681-11ce-4996-bf08-3d785067d50b

License:

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

History

Date received : 6 January 2022

Date accepted : 7 February 2022

Page count

Figures: 0, Tables: 0, Equations: 0, References: 13, Pages: 2, Words: 1378

Custom metadata

cover-date March 2022

Data availability:

Draft Genome Sequence of Plesiomonas shigelloides Strain PI-19, Isolated from the Intestine of Pufferfish (Tetraodon cutcutia)

Read this article at

ABSTRACT

Related collections

Genome Integrity

Most cited references 12

Trimmomatic: a flexible trimmer for Illumina sequence data

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

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

Author and article information

Contributors

Journal

Affiliations

Author notes

Author information

Article

History

Page count

Categories

Custom metadata

Comments

Comment on this article

Similar content 147

Most referenced authors 305