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

PROJECT phobi
Seals: a potential source of bacterial and viral fecal contamination of the littoral? 

PUBLICATION
Published to ENA under the accession number PRJEB64019.
See: https://www.ebi.ac.uk/ena/browser/view/PRJEB64019

DOI: https://doi.org/10.12770/76beca06-ac02-49ce-810e-94f9c121e868

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/dna-sequence-raw and data/rna-sequence-raw folders.
Metadata are located in data/report/athena/phobi_new and data/report/athena/phobi_viral where one can find 2021_16S-metagenomics-sequencing_PHOBI_NEW.xlsx and 2021_viral-metagenomics-sequencing_PHOBI.xlsx Excel files.
Metadata are also accessible through data/report/athena/phobi_new/XML and data/report/athena/phobi_viral/XML XML files.

DATA RETRIEVAL
wget -r -np -nH --cut-dirs=4 ftp://ftp.ifremer.fr/ifremer/dataref/bioinfo/sg2m/phobi

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.