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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Update on RefSeq microbial genomes resources.

Tatiana Tatusova1, Stacy Ciufo2, Scott Federhen2

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A 8600 Rockville Pike, Bethesda, MD 20894, USA. tatiana@ncbi.nlm.nih.gov.

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Summary
This summary is machine-generated.

The NCBI RefSeq genome collection now includes nearly 30,000 prokaryotic genomes, with over 10,000 added in 2014. Enhancements improve data access, analysis, and visualization tools for microbial genomics.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial Ecology

Background:

  • The National Center for Biotechnology Information (NCBI) RefSeq genome collection encompasses all major domains of life, including Eukarya, Bacteria, Archaea, and Viruses.
  • Prokaryotic genome sequences represent the fastest-growing segment of this collection.
  • In 2014, over 10,000 microbial genome assemblies were publicly released, increasing the total number of prokaryotic genomes to nearly 30,000.

Purpose of the Study:

  • To enhance the quality and usability of microbial genome resources.
  • To provide improved access to genomic data and pre-computed analysis results.
  • To advance analysis and visualization tools for microbial genomics.

Main Methods:

  • Improvements were made to the Prokaryotic Genome Annotation Pipeline.
  • New features were integrated into the RefSeq prokaryotic genomes data processing pipeline.
  • Optimization of protein cluster generation using a pan-genome approach was implemented.

Main Results:

  • The Prokaryotic Genome Annotation Pipeline has undergone several enhancements.
  • New functionalities have been added to the RefSeq prokaryotic genomes data processing pipeline.
  • Genome groups (clades) are now calculated, and protein cluster generation is optimized.

Conclusions:

  • The NCBI RefSeq database provides a comprehensive and improving resource for prokaryotic genomics.
  • Enhanced tools and data processing pipelines facilitate microbial genome analysis and discovery.
  • Ongoing development ensures better access and utility of microbial genome data for researchers.