Welcome on the Database

Here you can access to some view of our database:

Website Explanations

Overall Website Organization

Website Organization

Database Organization

Jobs Manager Organization

How upload Metadata ?

1 - "Import Data" Page : This Page contains all links and information for any Upload actions.
2 - "Metadata" files links : These links give Empty and non-empty file in csv (Comma Separated Value) and xlsx format.
3 - "Read Me" files : These file in French and in English resume the metadata information allowed in teh metadata file.
4 - "Search" button : This button allows searching and select the metadata file in your folder.
5 - "Start Upload" Button : This buttons allows to start the upload process to the website and the add-in database of the meta-datas.

Database Explanations

Setting database

This table show the species treat in our pipeline "ReadMapper" for the MLST Database.
And the default genes subset for ARM, Rep and Vir Detection in "ReadMapper" and "SeqDetector" pipeline (ARM)

Setting Database

Taxonomy Pipeline

This pipeline use Centrifuge tool to perform a taxonomy identification.

Here the list of species present in the centrifuge database:

Taxonomy Database

Plasmid Taxonomy Pipeline

This pipeline use Centrifuge tool to perform a taxonomy identification.

Here the list of plasmids present in the centrifuge-plasmids database:

Plasmid Database

Pipelines Explanations

ReadMapper Pipeline

This pipeline use ARIBA tool to perform a quick detection of MLST, ARM, Rep and Vir information present in a strain

* The genes found by Ariba are blast again our database to be confident about the ariba results.

ST Score and MLST Schemas

The ST score is a value pre-allowed of each previous MLST schemas identified in public database.

The MLST schemas is constituted by few (~ 5-7) genes who have these particularities:

- The gene is present in all individual of the species targeted

- The gene can discriminate complex inside the species targeted

The MLST schemas are created via the "pubmlstget" for ariba software

A Sequence Type (ST) score of "O" mean that the ST can not be addressed

SeqDetector Pipeline

This pipeline use DIAMOND tool to perform a quick detection of ARM information present in an assembly strain

SeqAssembler Pipeline

This table show the species treat in our pipeline "ReadMapper" for the MLST Database. And the default genes subset for ARM, Rep and Vir Detection in "ReadMapper" and "SeqDetector" pipeline (ARM)

This pipeline use Centrifuge tool to perform a taxonomy identification.

Here the list of species present in the centrifuge database:

This pipeline use Centrifuge tool to perform a taxonomy identification.

Here the list of plasmids present in the centrifuge-plasmids database:

This pipeline use ARIBA tool to perform a quick detection of MLST, ARM, Rep and Vir information present in a strain

* The genes found by Ariba are blast again our database to be confident about the ariba results.

The ST score is a value pre-allowed of each previous MLST schemas identified in public database.

The MLST schemas is constituted by few (~ 5-7) genes who have these particularities:

- The gene is present in all individual of the species targeted

- The gene can discriminate complex inside the species targeted

The MLST schemas are created via the "pubmlstget" for ariba software

A Sequence Type (ST) score of "O" mean that the ST can not be addressed

This pipeline use DIAMOND tool to perform a quick detection of ARM information present in an assembly strain

This pipeline use a5 and Spades tools to perform the best assembly possible

This table show the species treat in our pipeline "ReadMapper" for the MLST Database.
And the default genes subset for ARM, Rep and Vir Detection in "ReadMapper" and "SeqDetector" pipeline (ARM)