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

PROJECT ecomine
ECOMINE, Influence of mining massifs on the evolution of coastal microbial communities: eDNA as a tool for detecting environmental changes

PUBLICATION
Published to ENA under the accession number PRJEB76493.
See: https://www.ebi.ac.uk/ena/browser/view/PRJEB76493

DOI: https://doi.org/Undefined

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.
Metadata are located in data/report/athena where one can find 2022_ECOMINE_metabarcoding.xlsx Excel file.
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/dyneco/ecomine

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.