ABYSS_16S

Bioinformatics analysis and reproducible workflows for microbial ecogenomics of the benthic communities of the Mediterranean - Atlantic transition

In this repository you will find the scripts necessary to replicate the results shown in the following paper: Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean—Atlantic Gradient

• The raw data can be accessed here on ENA and here on the Ifremer reference server

• Processing of the raw reads was done using custom scripts on the Ifremer high-performance cluster. The currently updated pipeline can be found on this gitlab. An archive of the scripts used for this study are available here and the corresponding config files are available on this github space in folder Config_files

• The results of the processing up to the ASV and taxonomy table, including intermediary files, are available here

• This R script presents the reproducible statistical analysis of the 16S metabarcoding dataset. The metadata table used is Table S1 included in the paper.