KOunt – A reproducible KEGG orthologue abundance workflow

Jennifer Mattock; Marina Martínez-Álvaro; Matthew A. Cleveland; Rainer Roehe; Mick Watson

doi:10.1093/bioinformatics/btad483

KOunt – A reproducible KEGG orthologue abundance workflow

Jennifer Mattock^*, Marina Martínez-Álvaro, Matthew A. Cleveland, Rainer Roehe, Mick Watson

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

SUMMARY: Accurate gene prediction is essential for successful metagenome analysis. We present KOunt, a Snakemake pipeline, that precisely quantifies KEGG orthologue abundance.

AVAILABILITY AND IMPLEMENTATION: KOunt is available on GitHub: https://github.com/WatsonLab/KOunt. The KOunt reference database is available on figshare: https://doi.org/10.6084/m9.figshare.21269715. Test data are available at https://doi.org/10.6084/m9.figshare.22250152 and version 1.2.0 of KOunt at https://doi.org/10.6084/m9.figshare.23607834.

Original language	English
Article number	btad483
Pages (from-to)	1-3
Number of pages	3
Journal	Bioinformatics
Volume	39
Issue number	8
Early online date	8 Aug 2023
DOIs	https://doi.org/10.1093/bioinformatics/btad483
Publication status	E-pub ahead of print - 8 Aug 2023

Keywords / Materials (for Non-textual outputs)

Databases, Factual
Metagenome
Software
Workflow

Access to Document

10.1093/bioinformatics/btad483Licence: Other

btad483Final published version, 1.14 MBLicence: Creative Commons: Attribution (CC-BY)

1 Finished
1 Active

Identifying the genomic basis of complex traits in farmed animals
Headon, D. (Principal Investigator)
1/04/23 → 31/03/28
Project: Research
Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria
Watson, M. (Principal Investigator)
BBSRC
1/04/19 → 31/03/22
Project: Research

Cite this

@article{ee4f2284ba22421d81b69202e7db2190,

title = "KOunt – A reproducible KEGG orthologue abundance workflow",

abstract = "SUMMARY: Accurate gene prediction is essential for successful metagenome analysis. We present KOunt, a Snakemake pipeline, that precisely quantifies KEGG orthologue abundance.AVAILABILITY AND IMPLEMENTATION: KOunt is available on GitHub: https://github.com/WatsonLab/KOunt. The KOunt reference database is available on figshare: https://doi.org/10.6084/m9.figshare.21269715. Test data are available at https://doi.org/10.6084/m9.figshare.22250152 and version 1.2.0 of KOunt at https://doi.org/10.6084/m9.figshare.23607834.",

keywords = "Databases, Factual, Metagenome, Software, Workflow",

author = "Jennifer Mattock and Marina Mart{\'i}nez-{\'A}lvaro and Cleveland, {Matthew A.} and Rainer Roehe and Mick Watson",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2023. Published by Oxford University Press.",

year = "2023",

month = aug,

day = "8",

doi = "10.1093/bioinformatics/btad483",

language = "English",

volume = "39",

pages = "1--3",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "8",

}

TY - JOUR

T1 - KOunt – A reproducible KEGG orthologue abundance workflow

AU - Mattock, Jennifer

AU - Martínez-Álvaro, Marina

AU - Cleveland, Matthew A.

AU - Roehe, Rainer

AU - Watson, Mick

N1 - Publisher Copyright: © The Author(s) 2023. Published by Oxford University Press.

PY - 2023/8/8

Y1 - 2023/8/8

N2 - SUMMARY: Accurate gene prediction is essential for successful metagenome analysis. We present KOunt, a Snakemake pipeline, that precisely quantifies KEGG orthologue abundance.AVAILABILITY AND IMPLEMENTATION: KOunt is available on GitHub: https://github.com/WatsonLab/KOunt. The KOunt reference database is available on figshare: https://doi.org/10.6084/m9.figshare.21269715. Test data are available at https://doi.org/10.6084/m9.figshare.22250152 and version 1.2.0 of KOunt at https://doi.org/10.6084/m9.figshare.23607834.

AB - SUMMARY: Accurate gene prediction is essential for successful metagenome analysis. We present KOunt, a Snakemake pipeline, that precisely quantifies KEGG orthologue abundance.AVAILABILITY AND IMPLEMENTATION: KOunt is available on GitHub: https://github.com/WatsonLab/KOunt. The KOunt reference database is available on figshare: https://doi.org/10.6084/m9.figshare.21269715. Test data are available at https://doi.org/10.6084/m9.figshare.22250152 and version 1.2.0 of KOunt at https://doi.org/10.6084/m9.figshare.23607834.

KW - Databases, Factual

KW - Metagenome

KW - Software

KW - Workflow

U2 - 10.1093/bioinformatics/btad483

DO - 10.1093/bioinformatics/btad483

M3 - Article

C2 - 37535671

SN - 1367-4803

VL - 39

SP - 1

EP - 3

JO - Bioinformatics

JF - Bioinformatics

IS - 8

M1 - btad483

ER -

KOunt – A reproducible KEGG orthologue abundance workflow

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

Identifying the genomic basis of complex traits in farmed animals

Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria

Cite this