INTRODUCTION
This directory is part of the official repository of public bioinformatics
data sets available from IFREMER research teams.

PROJECT WGS_Vinseq
Whole genome sequencing of Vibrio bathopelagicus clones isolated from Paramoeba atlantica, 2023

PUBLICATION
Published to ENA under the accession number PRJEB83724.
See: https://www.ebi.ac.uk/ena/browser/view/PRJEB83724

DOI: 

DATA ORGANIZATION
Project is organized as follows: data is distributed
within several sub-folders all of them being named using the
EDAM Ontology (https://www.ebi.ac.uk/ols/ontologies/edam).
 
1/ Raw data is available from the 'data' sub-folder.

2/ Results from processing raw data is available in 'operation' sub-folder.

3/ In turn, sub-folders within 'data' and 'operation' rely on EDAM terms
depending on data type (data sub-folder) or operation type (operation
sub-folder).

DIRECTORY CONTENT
Raw fastq files are located in data/raw-sequence folder.
Genome asembly files are located in operation/genome-assembly folder.
Raw data metadata are located in data/report/athena folder where one can find 2023_WGS_Vinseq_public.xlsx Excel file.
Genome assembly metadata are located in operation/report/genome-assembly folder.
Metadata are also accessible through data/report/athena/XML XML files.

DATA RETRIEVAL
wget -r -np -nH --cut-dirs=4 ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/ihpe/WGS_Vinseq

Command-line explained:

          -r: is for recursively download;
         -np: is for no parent ascending;
         -nH: is for disabling creation of directory having name same as URL i.e. ftp.ifremer.fr;
  --cut-dirs: is for ignoring number of parent directories.
see https://data-dataref.ifremer.fr/bioinfo/ifremer/README.txt for more details.