The South American MicroBiome Archive (SAMBA)

Overview

The South American MicroBiome Archive (SAMBA) is the result of a semi-automated search and automated analysis of microbiome studies characterising the gut microbiome of people living in South America. The files here available are the result of using this workflow available in GitHub. The generated files (shared and described below) were then analysed conducting to the accompaining research article [INSERT LINK/DOI]. The code used to generate the figures of that analysis is available in this independent GitHub repository.

File description

Below there is the list of files shared in this repository, along with their respective description:

input_samba_v0.1.0.txt :                        List of accession codes for samples and bioprojects included in SAMBA.

asv_count_table_v0.1.0.tsv :                   ASV-level count table generated after the consolidation of all projects into one table.

genus_count_table_v0.1.0.tsv :              Genus-level count table generated after the consolidation of all projects into one table.

clean_genus_count_table_v0.1.0.tsv :    Genus-level count table after filtering low quality taxa and samples (Generated from genus_count_table_v0.1.0.tsv).

ASVs_v0.1.0.fasta :                                 ASV-sequences for all projects included in SAMBA.

metadata_v0.1.0.tsv :                             Metadata collected from INSDC and manually retrieved.