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KBase Narrative - Genomes of nine cultured microbes from two hydrologically connected freshwater sites in Wellesley MA

Dataset ·
 [1]
  1. Univ. of California, Riverside, CA (United States); Oak Ridge National Laboratory
We present the genomes of nine cultured microbes isolated from two freshwater sites in Wellesley, MA. The dataset is useful for exploring genomic diversity among freshwater taxa including Pedobacter, Pseudomonas, Rhodoferax, Rouxiella, and Flavobacterium.
Research Organization:
U.S. Department of Energy Systems Biology Knowledgebase
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI ID:
2404396
Country of Publication:
United States
Language:
English

References (13)

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
Trimmomatic: a flexible trimmer for Illumina sequence data journal April 2014
Assembly of long, error-prone reads using repeat graphs journal April 2019
Metagenome-assembled genome extraction and analysis from microbiomes using KBase journal November 2022
Prokka: rapid prokaryotic genome annotation journal March 2014
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal May 2015
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
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree journal October 2010
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
Polypolish: Short-read polishing of long-read bacterial genome assemblies journal January 2022
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal March 2010

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