├── .gitignore ├── Makefile ├── README.rst ├── cog-sum-mean-cov.tsv ├── in-house ├── bam_hist.sh ├── genes.to.kronaTable.py ├── get.prokka.annotation.sh ├── get_coverage_for_genes.py ├── prokkagff2bed.sh ├── prokkagff2gtf.sh └── tpm_table.py ├── reference_db ├── cog │ ├── cat.hierarchy │ └── cog.to.cat ├── kegg │ ├── ec.to.pwy │ └── pwy.hierarchy └── metacyc │ ├── ec.to.pwy │ └── pwy.hierarchy ├── requirements.txt ├── source ├── 16S-analysis │ ├── 16S_analysis.rst │ └── index.rst ├── annotation │ ├── functional-annotation │ │ ├── minpath.rst │ │ ├── prokka.rst │ │ └── read_mapping.rst │ ├── functional_annotation.rst │ ├── index.rst │ ├── quantification.rst │ ├── summarize.rst │ └── taxonomic_annotation.rst ├── assembly │ ├── assembly.rst │ └── index.rst ├── conf.py ├── index.rst ├── introduction.rst ├── login_uppmax.rst ├── reads-qc │ ├── fastqc.rst │ ├── index.rst │ └── qtrim.rst ├── reqs.rst ├── sample-comparison │ └── index.rst └── taxonomic-classification │ ├── diamond.rst │ ├── index.rst │ └── phylosift.rst ├── sum_rdp_annot.pl ├── summary.rrna.silva-bac-16s-database-id85.fasta.class.0.80.tsv └── test_all.sh /.gitignore: -------------------------------------------------------------------------------- 1 | *.swp 2 | build 3 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/metagenomics-workshop/HEAD/Makefile -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/metagenomics-workshop/HEAD/README.rst -------------------------------------------------------------------------------- /cog-sum-mean-cov.tsv: -------------------------------------------------------------------------------- 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