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

PROJECT searse
SEARSE project: metabarcoding data (V4-18S, V4V5-16S) in seawater surface of the New Caledonia lagoon

PUBLICATION
Published to ENA under the accession number PRJEB66118 (currently private)
doi: https://doi.org/10.12770/26840434-8354-4856-9d5e-e562c8de7252

DATA ORGANISATION
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
The directory of each sample is detailed in the report. 
The year corresponds to the arrival of the raw sequences and not to the time of sampling. 

In summary the sequences can be found at the following paths:
 - September 2019 / protist : "data/dna-sequence-raw/2019/protist"
 - September 2019 / bacteria (16S V3-V4) : "data/dna-sequence-raw/2019/bacteria"
 - September 2019 / bacteria (16S V4-V5) : "data/dna-sequence-raw/2020/bacteria"
 - February 2020 / protist : "data/dna-sequence-raw/2020/protist"
 - February 2020 / bacteria (16S V4-V5) : "data/dna-sequence-raw/2020/bacteria"
 - December 2020 / protist : "data/dna-sequence-raw/2020/protist"
 - December 2020 / bacteria (16S V4-V5) : "data/dna-sequence-raw/2021/bacteria"

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

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.