├── LICENSE ├── README.md ├── amr.sh ├── annotate.sh ├── assemble.sh ├── dendogram.sh ├── download_data.sh ├── environment.yaml ├── extract_annot_info.py ├── extract_reordered.py ├── gene_count_summary.py ├── genomes ├── Agy99.fasta ├── H37Rv.fasta ├── Liflandii.fasta ├── SGL03.fasta └── Shinsuense.fasta ├── get_annot_stats.py ├── get_genome_gffs.sh ├── get_pangenome.sh ├── get_pseudo.pl ├── mlst.sh ├── pip-requirements.txt ├── polish.sh ├── qc_assembly.sh ├── qc_raw_reads.sh ├── qc_trimmed_reads.sh ├── ragtag_analysis.py ├── reorder_contigs.sh ├── roary_plots.py ├── trim_reads.sh └── zip_results.sh /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vappiah/bacterial-genomics-tutorial/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/vappiah/bacterial-genomics-tutorial/HEAD/trim_reads.sh -------------------------------------------------------------------------------- /zip_results.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | zip -r results QC_* P7741* mlst.csv amr.summary.tab dendogram pangenome *.jpg 4 | 5 | --------------------------------------------------------------------------------