Caribou-Bone-Degradation

Set of scripts and data to analyse the genomic and metagenomic data from the Høier-Eriksen et al., 2024 paper

ANVI'O CONTIGS.DB used plus the FASTA files of the MAGs can be further downloaded from: https://sid.erda.dk/cgi-sid/ls.py?share_id=CiQxxrCu9l

Name		Name	Last commit message	Last commit date
Latest commit History 6 Commits
ADDITIONAL_DATA		ADDITIONAL_DATA
01_anvio_2021_config.json		01_anvio_2021_config.json
02_anvio_1978_config.json		02_anvio_1978_config.json
ANNOTATE_metabolism_per_CONTIGS_DB.sbatch		ANNOTATE_metabolism_per_CONTIGS_DB.sbatch
Anvio_launch_snakemake_workflow.sbatch		Anvio_launch_snakemake_workflow.sbatch
ESTIMATE_metabolism_per_CONTIGS_DB.sbatch		ESTIMATE_metabolism_per_CONTIGS_DB.sbatch
MAGs_diversity_1978-2021_DESeq.R		MAGs_diversity_1978-2021_DESeq.R
MAGs_diversity_bones-soil.R		MAGs_diversity_bones-soil.R
README.md		README.md
anvio_metabolism_functions_per_sample.R		anvio_metabolism_functions_per_sample.R
dereplicate_MAGs.sbatch		dereplicate_MAGs.sbatch
format_gtdbtk_MAGs_taxonomy.sbatch		format_gtdbtk_MAGs_taxonomy.sbatch
gen_functions_across_genomes.sbatch		gen_functions_across_genomes.sbatch
gtdbtk_MAGs_taxonomy.sbatch		gtdbtk_MAGs_taxonomy.sbatch
krakenuniq_alpha-diversity.R		krakenuniq_alpha-diversity.R
krakenuniq_bracken.sbatch		krakenuniq_bracken.sbatch
metaDMG2_analysis_stats_paper_plots.R		metaDMG2_analysis_stats_paper_plots.R
metaDMG2_bowtieMAP.sbatch		metaDMG2_bowtieMAP.sbatch
metaDMG2_compute.sbatch		metaDMG2_compute.sbatch
metaDMG2_indexMAGs.sbatch		metaDMG2_indexMAGs.sbatch
metaDMG2_plots.R		metaDMG2_plots.R

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