The IMG/M data management and analysis system v.7: content updates and new features

Chen, I-Min A.; Chu, Ken; Palaniappan, Krishnaveni; Ratner, Anna; Huang, Jinghua; Huntemann, Marcel; Hajek, Patrick; Ritter, Stephan J; Webb, Cody; Wu, Dongying; Varghese, Neha J; Reddy, T. K.; Mukherjee, Supratim; Ovchinnikova, Galina; Nolan, Matt; Seshadri, Rekha; Roux, Simon; Visel, Axel; Woyke, Tanja; Eloe-Fadrosh, Emiley A; Kyrpides, Nikos C; Ivanova, Natalia N

doi:10.1093/nar/gkac976

The IMG/M data management and analysis system v.7: content updates and new features

Journal Article · Wed Nov 16 00:00:00 EST 2022 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkac976· OSTI ID:1907597

^[1]; Chu, Ken ^[1]; Palaniappan, Krishnaveni ^[1]; Ratner, Anna ^[1]; Huang, Jinghua ^[1]; ^[1]; Hajek, Patrick ^[1]; Ritter, Stephan J ^[1]; Webb, Cody ^[1]; Wu, Dongying ^[1]; Varghese, Neha J ^[1]; ^[1]; ^[1]; ^[1]; Nolan, Matt ^[1]; Seshadri, Rekha ^[1]; ^[1]; Visel, Axel ^[1]; Woyke, Tanja ^[1]; ^[1] more »

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute

The Integrated Microbial Genomes & Microbiomes system at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. Here, we also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1907597

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 51; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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