RRAP: RPKM Recruitment Analysis Pipeline

A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automa...

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Detalles Bibliográficos
Autores principales: Kojima, Conner Y., Getz, Eric W., Thrash, J. Cameron
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2022
Materias:
Databases and Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9476942/
https://www.ncbi.nlm.nih.gov/pubmed/35993706
http://dx.doi.org/10.1128/mra.00644-22
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author Kojima, Conner Y.
Getz, Eric W.
Thrash, J. Cameron
author_facet Kojima, Conner Y.
Getz, Eric W.
Thrash, J. Cameron
author_sort Kojima, Conner Y.
collection PubMed
description A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools.
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spelling pubmed-94769422022-09-16 RRAP: RPKM Recruitment Analysis Pipeline Kojima, Conner Y. Getz, Eric W. Thrash, J. Cameron Microbiol Resour Announc Databases and Software A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools. American Society for Microbiology 2022-08-22 /pmc/articles/PMC9476942/ /pubmed/35993706 http://dx.doi.org/10.1128/mra.00644-22 Text en Copyright © 2022 Kojima et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Databases and Software
Kojima, Conner Y.
Getz, Eric W.
Thrash, J. Cameron
RRAP: RPKM Recruitment Analysis Pipeline
title RRAP: RPKM Recruitment Analysis Pipeline
title_full RRAP: RPKM Recruitment Analysis Pipeline
title_fullStr RRAP: RPKM Recruitment Analysis Pipeline
title_full_unstemmed RRAP: RPKM Recruitment Analysis Pipeline
title_short RRAP: RPKM Recruitment Analysis Pipeline
title_sort rrap: rpkm recruitment analysis pipeline
topic Databases and Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9476942/
https://www.ncbi.nlm.nih.gov/pubmed/35993706
http://dx.doi.org/10.1128/mra.00644-22
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