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Isolate genomes from "Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance"

Dataset ·
 [1];  [2]; ; ;  [3]; ; ;  [3];  [3];  [4];  [3];
  1. KBase
  2. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance. This Narrative contains data for the 261 ENIGMA isolates described in the paper. See Table S2 for a complete list.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
DOE Contract Number:
AC02-05CH11231
OSTI ID:
1637360
Country of Publication:
United States
Language:
English

References (12)

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
A complete domain-to-species taxonomy for Bacteria and Archaea journal April 2020
Trimmomatic: a flexible trimmer for Illumina sequence data journal April 2014
Accelerated Profile HMM Searches journal October 2011
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing journal May 2012
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries journal November 2018
Cutadapt removes adapter sequences from high-throughput sequencing reads journal May 2011
Prodigal: prokaryotic gene recognition and translation initiation site identification journal March 2010
Prokka: rapid prokaryotic genome annotation journal March 2014
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments journal March 2010
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life journal August 2018
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree journal October 2010


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