This repository contains code and supplementary materials for the AlKoSol project's shotgun metagenomics data analysis. The data and metadata are organized using the pISA-tree research data management framework.
Official project web page: https://projects.nib.si/alkosol/
SICRIS project web page: https://cris.cobiss.net/ecris/en/en/project/19991
Shotgun metagenomic raw sequencing reads are available at SRA under BioProject accession number PRJNA1225550.
The wet lab DNA protocol for DNA isolation is available here: _I_SecoveljskeSoline/_S_DNA_seq/_A_01-gDNAisol/Protocols.
The sample metadata is stored in the _I_SecoveljskeSoline/phenodata_20230306.xlsx.
The command for running the classification with Centrifuge and Recentrifuge is available here _I_SecoveljskeSoline/_S_DNA_seq/_A_03_TaxClass-dry/scripts/soline_centrifuge_rcf_commands.txt.
The results of the Centrifuge classification are available in the directory _I_SecoveljskeSoline/_S_DNA_seq/_A_03_TaxClass-dry/output/centrifuge.
The interactive Krona plots produced by Recentrifuge are available in the directory _I_SecoveljskeSoline/_S_DNA_seq/_A_03_TaxClass-dry/output/rcf_summary. Download the HTML files and open in a web browser to explore the Krona plots.
The results of the differential abundance analysis for taxon assignments of reads are available here:
- MaAsLin2_LM -- MaAsLin2 linear model fit
- MaAsLin2_NEGBIN -- MaAsLin2 negative binomial model fit
- voomLmFit -- EdgeR voom linear model fit
The R script (Rmd file) and the corresponding HTML report generated by the script are available here: _I_SecoveljskeSoline/_S_DNA_seq/_A_03_TaxClass-dry/scripts