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KBase Narrative - Timberlake Metagenomes

Dataset ·
 [1];  [2];  [3];  [4]
  1. Joint Genome Institute JGI; Oak Ridge National Laboratory
  2. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
  3. Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
  4. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

This narrative contains the MAG Analysis from: Clifton P Bueno de Mesquita, Wyatt H Hartman, Marcelo Ardón, Susannah G Tringe, Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland, ISME Communications, 2024; ycae040, https://doi.org/10.1093/ismeco/ycae040 Metagenomes were uploaded to IMG/M for other analyses.

Research Organization:
U.S. Department of Energy Systems Biology Knowledgebase
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
DOE Contract Number:
AC02-05CH11231
OSTI ID:
2336591
Country of Publication:
United States
Language:
English

References (41)

KBase: The United States Department of Energy Systems Biology Knowledgebase journal July 2018
GTDB-Tk v2: memory friendly classification with the genome taxonomy database journal October 2022
Binning metagenomic contigs by coverage and composition journal September 2014
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal November 2013
Identification, variation and transcription of pneumococcal repeat sequences journal February 2011
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies journal May 2012
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities journal January 2015
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes journal February 2015
Microbial species delineation using whole genome sequences journal July 2015
Metagenome-assembled genome extraction and analysis from microbiomes using KBase journal November 2022
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland journal March 2024
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
Translational recoding in archaea journal September 2012
SMART: recent updates, new developments and status in 2015 journal October 2014
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life journal August 2018
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy journal September 2021
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system journal October 2016
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree journal October 2010
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes journal January 2007
Versatile and open software for comparing large genomes journal January 2004
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
Identifying bacterial genes and endosymbiont DNA with Glimmer journal January 2007
The RAST Server: Rapid Annotations using Subsystems Technology journal January 2008
Mash: fast genome and metagenome distance estimation using MinHash journal June 2016
The Pfam protein families database: towards a more sustainable future journal December 2015
Accelerated Profile HMM Searches journal October 2011
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets journal October 2015
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm journal August 2014
BLAST+: architecture and applications journal January 2009
BLAT---The BLAST-Like Alignment Tool journal March 2002
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
20 years of the SMART protein domain annotation resource journal October 2017
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal March 2010
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation journal May 2018
dRep: A tool for fast and accurate genome de-replication that enables tracking of microbial genotypes and improved genome recovery from metagenomes preprint February 2017
FIGfams: yet another set of protein families journal September 2009
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures journal November 2016
TIGRFAMs and Genome Properties in 2013 journal November 2012
Fast and accurate short read alignment with Burrows-Wheeler transform journal May 2009
A Genomic Perspective on Protein Families journal October 1997

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