Genome assembly PDT001787794.1

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Submitted GenBank assembly
GCA_030721285.1
Taxon
Cronobacter sakazakii
Strain
2020N-4002
WGS project
ABLPRF01
Submitter
PulseNet Next Generation Subtyping Methods Unit
Date
Aug 14, 2023

Genome notes

NCBI has noted the following for this genome assembly. View definitions

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size4.4 Mb
Total ungapped length4.4 Mb
Number of contigs97
Contig N50119.5 kb
Contig L5012
GC percent57
Genome coverage46.0x
Assembly levelContig

Sample details

BioSample ID
SAMN35880110
Description
Cronobacter sakazakii
Submitter
Centers for Disease Control and Prevention Enteric Diseases Laboratory Branch
Strain
2020N-4002
Source type
human
Collection date
2019
Project name
PulseNet
Sequenced by
CDC
SRA
SRS18049973
EDLB-CDC
2020N-4002
Models
Pathogen.cl
Package
Pathogen.cl.1.0
Submission date
2023-06-23T14:31:07.300
Publication date
2023-06-23T00:00:00.000
Last updated
2023-06-23T14:35:21.483

Assembly methods

Sequencing technology
ILLUMINA
Comment

The annotation was added by the assembly submitters using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about stand-alone PGAP can be found here: https://github.com/ncbi/pgap/

This draft WGS assembly was generated by running SKESA to generate a de-novo assembly. The de-novo assembly was then concatenated with contigs generated using a guided assembler using antimicrobial resistance genes as baits to comprehensively catalog the set of resistance genes in the isolate. Note, some parts of the contigs derived from the guided assembler may overlap de-novo contigs, and other guided assembler contigs. De-novo contigs can be differentiated from guided assembler contigs by their names , which include either 'denovo' or 'guided'.

Assembly method
SKESA v. 2.2

Additional genomes

Browse all Cronobacter sakazakii genomes (2271)

BioProject

PRJNA420465

Cronobacter Genome sequencing and assembly

Pathogen Detection Resource

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJun 23, 2023
Genes4,168
Protein-coding4,000
Software version2021-01-11.build5132

About PGAP

The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) uses multiple approaches to predict protein-coding and RNA genes and other functional elements directly from sequence.

Continue reading

Quality analysis

Taxonomy check

Taxonomy check status
OK
Best match status
species_match
Submitted organism name
Cronobacter sakazakii
Submitted species name
Cronobacter sakazakii

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_000684935.1GCA_000684935.1
Organism nameCronobacter sakazakii NBRC 102416Cronobacter sakazakii
Type categorytypetype
ANI98.04%98.04%
Assembly coverage91.32%91.32%
Type assembly coverage88.58%88.58%

Chromosomes

Note: This contig-level genome assembly includes 97 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_030721285.1

n/a

PDT001787794.1ContigAug 14, 2023