CCMP: software-as-a-service approach for fully-automated microbiome profiling.
Journal
Journal of biomedical informatics: X
ISSN: 2590-177X
Titre abrégé: J Biomed Inform X
Pays: United States
ID NLM: 101751572
Informations de publication
Date de publication:
Jun 2019
Jun 2019
Historique:
entrez:
5
9
2019
pubmed:
5
9
2019
medline:
5
9
2019
Statut:
ppublish
Résumé
Microbiome profiling holds great promise for the development of novel disease biomarkers and therapeutics. Next-generation sequencing is currently the preferred method for microbiome data collection and multiple standardized tools, packages, and pipelines have been developed for the purpose of raw data processing and microbial annotation. However, these currently available pipelines come with entry-level barriers such as high-performance hardware, software installation, and sequential command-line scripting that often deter end-users. We thus created Cloud Computing for Microbiome Profiling (CCMP, https://ccmp.usc.edu), a public cloud-based web tool which combines the analytical power of current microbiome analysis platforms with a user-friendly interface. CCMP is a free-of-charge software-as-a-service (SaaS) that simplifies user experience by enabling users to complete their analysis in a single step, uploading raw sequencing data files. Once users upload 16S ribosomal RNA gene sequence data, our pipeline performs taxonomic annotation, abundance profiling, and statistical tests to report microbiota signatures altered by diseases or experimental conditions. CCMP took a 125 gigabyte (GB) input of 16S ribosomal RNA gene sequence data from 1052 specimens in FASTQ format and reported figures and tables of taxonomic annotations, statistical tests,
Identifiants
pubmed: 31482150
doi: 10.1016/j.yjbinx.2019.100040
pmc: PMC6719681
mid: NIHMS1048076
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : NIAID NIH HHS
ID : R01 AI083115
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI095066
Pays : United States
Déclaration de conflit d'intérêts
Conflict of interest There is no conflict of interest.
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