- All environments, scripts and jupyter notebooks required to replicate the Ecosystems Under Cryospheric Influence analyses are here within
- Below are the individual folders, scripts and
Snakemake
files required to accomplish all the analyses in the manuscript
0_preprocessing
: All scripts required for preprocessing both amplicon and metagenomic (metag) dataenvs
: conda environments required for all analyses usingSnakemake
scripts
: custom and exisiting scripts for individual steps and certain preprocessing steps including utility and accessory scripts for downstream analyses
- Scripts and jupyter notebooks involved in the amplicon analyses include the following
- 0_preprocessing/PP1_classifer.sh
- 0_preprocessing/PP2_classifer.sh
- 0_preprocessing.R
- 1_Dataset_exploration.R
- 2_SVM_EUCI.ipynb
- 3_Specific_analysis.R
- 4_Taxonomic_analysis.R
- 5_Phylogenetics.R
- Scripts and
Snakemake
files required for metagenomic preprocessing and downstream analyses include the following:
- 0_preprocessing/IMP_config.yaml: example config file for running IMP analyses
- 0_preprocessing/metag_config.yaml: config file for preprocessing samples using IMP
- 0_preprocessing/slurm.yaml: SLURM configuration file for running the analyses on a HPC-environment
- 0_preprocessing/snakemake_parsable_launcher.sh: SBATCH launcher for running initial IMP preprocessing
- 6_MTG_taxonomy.R
- 7_MTG_functional.R
- 8_Functional_taxonomy.R
- 9_Genes_clustering.ipynb
- 9_Unassigned_genes.ipynb
- cluster_list: list of all clusters of KEGG+Unassigned genes based on "mmseqs2" analyses
- config.yaml: config file for running the initial gene fasta extraction and "mmseqs2" clustering
- coverage_Snakefile: to estimate coverage for each contig/gene in the assemblies
- coverage_config.yaml: config file required to run "coverage_Snakefile"
- extraction_Snakefile: to extract fasta sequences based on cluster IDs, get cluster stats, MAFFT alignment, consensus sequence selection and tRNA analyses.
- extraction_config.yaml: config file required to run "extraction_Snakefile"
- get_clusterID.sh: bash script to collect all contig IDs belonging to individual cluster IDs
- kegg_plus_unassigned_list: list of all unassigned genes, and KEGG IDs
- list: test list for testing Snakefiles
- sample_list: list of samples used for metaG analyses
- unassigned_clusters_EUCI.tsv: Tab-delimited file indicating which contig IDs belong to which respective clusters.