KOunt: a reproducible KEGG orthologue abundance workflow

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 datab...

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Detalles Bibliográficos
Autores principales: Mattock, Jennifer, Martínez-Álvaro, Marina, Cleveland, Matthew A, Roehe, Rainer, Watson, Mick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10423021/
https://www.ncbi.nlm.nih.gov/pubmed/37535671
http://dx.doi.org/10.1093/bioinformatics/btad483
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author Mattock, Jennifer
Martínez-Álvaro, Marina
Cleveland, Matthew A
Roehe, Rainer
Watson, Mick
author_facet Mattock, Jennifer
Martínez-Álvaro, Marina
Cleveland, Matthew A
Roehe, Rainer
Watson, Mick
author_sort Mattock, Jennifer
collection PubMed
description 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.
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spelling pubmed-104230212023-08-13 KOunt: a reproducible KEGG orthologue abundance workflow Mattock, Jennifer Martínez-Álvaro, Marina Cleveland, Matthew A Roehe, Rainer Watson, Mick Bioinformatics Applications Note 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. Oxford University Press 2023-08-03 /pmc/articles/PMC10423021/ /pubmed/37535671 http://dx.doi.org/10.1093/bioinformatics/btad483 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Mattock, Jennifer
Martínez-Álvaro, Marina
Cleveland, Matthew A
Roehe, Rainer
Watson, Mick
KOunt: a reproducible KEGG orthologue abundance workflow
title KOunt: a reproducible KEGG orthologue abundance workflow
title_full KOunt: a reproducible KEGG orthologue abundance workflow
title_fullStr KOunt: a reproducible KEGG orthologue abundance workflow
title_full_unstemmed KOunt: a reproducible KEGG orthologue abundance workflow
title_short KOunt: a reproducible KEGG orthologue abundance workflow
title_sort kount: a reproducible kegg orthologue abundance workflow
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10423021/
https://www.ncbi.nlm.nih.gov/pubmed/37535671
http://dx.doi.org/10.1093/bioinformatics/btad483
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