Introduction
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This directory contains data related to this publication:
https://doi.org/10.12770/bb811ad3-269a-4ff6-82d1-e9e41f3a9534 


PROJECT Valopolymer
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Blue Crab Portunis Segnis Microbiome - 16S rDNA metabarcoding

 The blue crab  Portunus segnis is an invasive species that has been colonizing the Tunisian coasts since 2014. It is currently marketed as a food, and we aim at exploring the associated bacterial diversity in order to open up new ways of valorization. In this study, different blue crab samples were collected from the coastal area of Sfax, Tunisia. Different parts of this shellfish, such as flesh, gills, viscera, carapace scraping sample, as well as three successive blue crab washing waters from the production plant were studied. Bacterial DNA was extracted from each fraction and sequenced using metabarcoding approach targeting the V3-V4 region of the 16S rDNA.  


Data organization
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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
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Raw fastq files are located in data/rna-sequence-raw folder.
Metadata are located in data/report/athena where one can find 2022_16S-profiling_valopolymer.xlsx Excel file.
Metadata are also accessible through data/report/athena/XML XML files.


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

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.