Pacific Biosciences of California Inc (PACB)

[Paulieme]

Public Health England reference collections

This project aims to provide annotated and assembled genomes for 3,000 bacteria and 500 viruses as part of a new eResource

The project is split into two parts:

NCTC 3000: A joint collaboration between Public Health England, Pacific Biosciences and the Wellcome Trust Sanger Institute to complete the sequencing of 3,000 bacterial strains from PHE's National Collection of Type Cultures (NCTC) using Pacific Biosciences' Single Molecule, Real-Time (SMRT) sequencing technology.

NCPV 500: A collaboration between PHE and Sanger to produce 500 viral genomes from PHE's National Collection of Pathogenic Viruses (NCPV) using the Illumina sequencing platform.

Collectively, the data generated will be housed in a publically accessible web-based eResource that integrates metadata and genome sequences for type and reference strains of biomedically important bacterial and viral pathogens. This resource will integrate accession, taxonomy and authentication information with publications, genome sequences, comparative analysis databases and other resources at EMBL and NCBI.

This is a community resource project. Data will be available from here, and from the NCTC. We will submit assembled, annotated sequences to the International Sequence Databases as they become available. We request that you cite this webpage in any publication using the data, and would appreciate it if you contact us to discuss the use of this data.

Data Downloads
•Download annotated assemblies#
•BLAST server

Please note: these are pre-submission assemblies that should not be treated as final versions. Assemblies contain both chromosomal and plasmid contigs.

Background

The Wellcome Trust Sanger Institute will generate PacBio sequencing data and provide assembled and annotated genomes for the 3,000 bacteria from the NCTC collection.

The NCTC is one of the world's premier collections for bacterial strains, but most bacteria in NCTC currently have no genome references. Biological Resource Centres, such as NCTC and NCPV, are a vital part of the infrastructure underpinning life sciences, providing biomaterials of known provenance. Type and reference strains act as landmarks for mapping microbial diversity and measuring unique changes in properties and patterns of infection and response to clinical interventions. Combining reference genomes with the wealth of historical and biological information existing for these strains will generate a data set of enormous value for basic and clinical microbiology.

Pacific Biosciences' Single Molecule, Real-Time (SMRT) Sequencing technology achieves very long reads and high consensus accuracy, greatly improving the ability to finish bacterial genomes. And, because the technology can directly detect base modifications, the epigenomes for bacteria can also be obtained with no additional data acquisition, and this data will also be provided.

NCTC Strains

As bacterial strains from the collection progress through the project, links to the raw sequence data, epigenome data and annotated assemblies will appear here.

Current Statistics
•Number of species sequenced: 158
•Number of samples:719
•Number of samples manually assembled:298
•Number of samples automatically assembled:81

http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/#t_2