ArticleStandards in genomic sciences2010
The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data.
Article in Standards in genomic sciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes.The ISME journal · 2018Article
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- High abundance and expression of transposases in bacteria from the Baltic Sea.The ISME journal · 2017Article
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- Transcriptome analysis of Streptococcus gordonii Challis DL1 indicates a role for the biofilm-associated fruRBA operon in response to Candida albicans.Molecular oral microbiology · 2016Article
- Draft Genome Sequence of a Multi-Metal Resistant BacteriumFrontiers in microbiology · 2016Article
- Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.PloS one · 2016Article
- Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.The ISME journal · 2015Article
- DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.BMC bioinformatics · 2015Article
- GRASP: guided reference-based assembly of short peptides.Nucleic acids research · 2015Article
- An overview of malaria transmission from the perspective of Amazon Anopheles vectors.Memorias do Instituto Oswaldo Cruz · 2015Review
- Developing of the Computer Method for Annotation of Bacterial Genes.Advances in bioinformatics · 2015Article
- Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa.Memorias do Instituto Oswaldo Cruz · 2014Review
- Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary.Genome announcements · 2014Article
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- Functional tradeoffs underpin salinity-driven divergence in microbial community composition.PloS one · 2014Article
- An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome.Microbiome · 2013Article
- Analytical tools and databases for metagenomics in the next-generation sequencing era.Genomics & informatics · 2013Review
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12 authors.
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Abstract
The JCVI metagenomics analysis pipeline provides for the efficient and consistent annotation of shotgun metagenomics sequencing data for sampling communities of prokaryotic organisms. The process can be equally applied to individual sequence reads from traditional Sanger capillary electrophoresis sequences, newer technologies such as 454 pyrosequencing, or sequence assemblies derived from one or more of these data types. It includes the analysis of both coding and non-coding genes, whether full-length or, as is often the case for shotgun metagenomics, fragmentary. The system is designed to provide the best-supported conservative functional annotation based on a combination of trusted homology-based scientific evidence and computational assertions and an annotation value hierarchy established through extensive manual curation. The functional annotation attributes assigned by this system include gene name, gene symbol, GO terms, EC numbers, and JCVI functional role categories.
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