Genome assembly PDT002101104.1

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Submitted GenBank assembly
GCA_037072305.1
Taxon
Staphylococcus pseudintermedius
Strain
SPSE-23-VL-SD-MI-0025
WGS project
ABQPNY01
Submitter
Vet-LIRN-CVM-FDA
Date
Mar 8, 2024

Genome notes

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

  • from large multi-isolate project

Assembly statistics

GenBank
Genome size2.6 Mb
Total ungapped length2.6 Mb
Number of contigs33
Contig N50276.1 kb
Contig L504
GC percent37.5
Genome coverage221.0x
Assembly levelContig

Sample details

BioSample ID
SAMN40262492
Description
One Health Enteric sample from Staphylococcus pseudintermedius
Submitter
Vet-LIRN Project: SDSU Veterinary & Biomedical Sciences/ DOH South Dakota
Strain
SPSE-23-VL-SD-MI-0025
Collected by
Michigan State University Veterinary Diagnostic Laboratory
Collection date
Sep 30, 2023
Geographic location
USA:MI
Isolation source
Foot
Source type
animal
Purpose of sampling
Monitoring
Host
Canis lupus familiaris
Host disease
Pyoderma
Project name
Vet-LIRN
Sequenced by
South Dakota State University|South Dakota Animal Disease Research and Diagnostic Laboratory
Sample name
SPSE-23-VL-SD-MI-0025
SRA
SRS20691527
Models
One Health Enteric
Package
OneHealthEnteric.1.0
Submission date
2024-03-05T10:45:07.987
Publication date
2024-03-05T00:00:00.000
Last updated
2024-03-07T16:53:40.797

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

Annotation details

GenBank
ProviderNCBI
NameNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateMar 8, 2024
Genes2,545
Protein-coding2,430
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.

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Quality analysis

Taxonomy check

Taxonomy check status
OK
Best match status
species_match
Submitted organism name
Staphylococcus pseudintermedius
Submitted species name
Staphylococcus pseudintermedius

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_001792775.2GCA_001792775.2
Organism nameStaphylococcus pseudintermediusStaphylococcus pseudintermedius
Type categorytypetype
ANI99.5%99.5%
Assembly coverage90.17%90.17%
Type assembly coverage94.07%94.07%

Chromosomes

Note: This contig-level genome assembly includes 33 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_037072305.1

n/a

PDT002101104.1ContigMar 8, 2024