Metagenome-Assembled Genomes from Photo-Oxidized and Nonoxidized Oil-Degrading Marine Microcosms

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 performed deep metagenomic sequencing on hydrocarbon-degrading marine microcosms designed to experimentally determine the effect of photo-oxidation on oil biodegradation dynamics. Assembly, binning, and dereplication yielded 73 unique metagenome-assembled genomes (MAGs) from 6 phyla, of which 61 are predicted to be over 90% complete.

Related collections

Most cited references 21

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 16584 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen, Yanqing Zhou, Yaru Chen … (2018)

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.

0 comments Cited 5964 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Dinghua Li, Chi-Man Liu, Ruibang Luo … (2015)

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

0 comments Cited 2073 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

J. Cameron Thrash:

ORCID: https://orcid.org/0000-0003-0896-9986

Frank J. Stewart: 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): 10 May 2023

Publication date (Electronic, collection): June 2023

Publication date PMC-release: 10 May 2023

Volume: 12

Issue: 6

Electronic Location Identifier: e00210-23

Affiliations

[a ] Department of Biological Sciences, University of Southern California, Los Angeles, California, USA

[b ] Department of Civil and Environmental Engineering, University of Southern California, Los Angeles, California, USA

[c ] Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA

[d ] Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA

Montana State University

Author notes

Raven C. Althouse, Bianca F. Costa, Boyan Hu, Maxim Kovalev, Timur Kulik, Yu-Tung Lee, Meredith C. Moore, Emily Peng, Jing Yao Pook, Akshita Sharma, and Celia Wood contributed equally to the work and are listed in alphabetical order by last name.

The authors declare no conflict of interest.

Author information

Eric A. Webb https://orcid.org/0000-0003-4085-7730

J. Cameron Thrash https://orcid.org/0000-0003-0896-9986

Article

Publisher ID: 00210-23 Publisher ID: mra.00210-23

DOI: 10.1128/mra.00210-23

PMC ID: 10281115

PubMed ID: 37162353

SO-VID: 5b546432-06d6-40c8-9556-485e8c9b68c9

License:

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

History

Date received : 15 March 2023

Date accepted : 24 April 2023

Page count

Figures: 0, Tables: 0, Equations: 0, References: 22, Pages: 3, Words: 1617

Funding

Funded by: National Academies of Sciences, Engineering, and Medicine (NASEM), FundRef https://doi.org/10.13039/100009643;

Award ID: Gulf Research Program Early Career Fellowship

Award Recipient : J. Cameron Thrash

Funded by: National Academies of Sciences, Engineering, and Medicine (NASEM), FundRef https://doi.org/10.13039/100009643;

Award ID: Gulf Research Program Early Career Fellowship

Award Recipient : Christoph Aeppli

Custom metadata

cover-date June 2023

Data availability:

Comments

Comment on this article

scite_

Cited by 1

Metabuli: sensitive and specific metagenomic classification via joint analysis of amino acid and DNA
Authors: Jaebeom Kim, Martin Steinegger

See all cited by

Most referenced authors 549

See all reference authors

Metagenome-Assembled Genomes from Photo-Oxidized and Nonoxidized Oil-Degrading Marine Microcosms

Read this article at

ABSTRACT

Related collections

G3: Genes|Genomes|Genetics

Most cited references 21

Trimmomatic: a flexible trimmer for Illumina sequence data

fastp: an ultra-fast all-in-one FASTQ preprocessor

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Author and article information

Contributors

Journal

Affiliations

Author notes

Author information

Article

History

Page count

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 56

Cited by 1

Most referenced authors 549