Building a Microbial Foods MAG dataset and a Microbial foods gene catalog

Here we are gathering code and documentation to build a microbial foods MAG dataset and a microbial foods gene catalog

We are uptdating documentation about all the datasets and samples considered.

There will be code:

• to study the diversity coverage of the different microbial foods MAG databases,
• to join and repreplicate MAG collections
• to build step by step the MAG datasets from internal samples
• to build a MAG-derived gene catalog
• to run some diversity and taxonomic analysis on internal samples using the resource created

Data included:

• cFMD
• MiFoDB
• Internal samples from Microbial Foods dept at DTU-Biosustain

Diversity coverage of the different microbial foods MAG databases

input files: .tsv files generated by CoverM

coverm_stats.R: R script from calculating and plotting relative abudance, alpha and beta diversity

diversity results : plots and tables created by the R script

Gene clustering statistics

gene_clustering_stats.py: python script for calculating gene redusancy statistics after clustering

HPC workflow creating gene catalog from pubicly avaible MAGs and internally constructed MAGs

gene_catalog.html: step-by-step guide for reating gene catalog from pubicly avaible MAGs and internally constructed MAGs

MAG set preprocessing for the pubibly avaible MAGs set

find_files.sh: Shell script for recursively locating files within complex directory structures produced by large workflows. Useful for managing outputs from multi-step pipelines.

tag_mags.sh: Shell script used to add standardized identifiers (e.g. sample or batch tags) to MAG filenames. This ensures consistent naming across downstream analyses and plots.

rename_headers.sh Shell script used to standardize FASTA headers for MAGs or gene sequences. This step is critical for: • Avoiding header-related issues in downstream tools • Ensuring compatibility across mapping, annotation, and visualization steps

Drep Clustering

plots generated by drep for the final dereplecation

NOTE : due to file size limitations,some files are available upon request.