├── .Rhistory ├── .gitignore ├── Makefile ├── README ├── make.bat ├── markdown ├── docs │ ├── 01_anthrax_comparative_analysis.md │ └── index.md ├── mkdocs.yml └── site │ ├── 01_anthrax_comparative_analysis │ └── index.html │ ├── 404.html │ ├── css │ ├── base.css │ ├── bootstrap-custom.css │ ├── bootstrap-custom.min.css │ ├── cinder.css │ ├── font-awesome-4.0.3.css │ └── highlight.css │ ├── fonts │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ └── fontawesome-webfont.woff │ ├── img │ ├── favicon.ico │ ├── grid1.png │ ├── grid10.png │ ├── grid11.png │ ├── grid12.png │ ├── grid13.png │ ├── grid14.png │ ├── grid15.png │ ├── grid16.png │ ├── grid17.png │ ├── grid18.png │ ├── grid19.png │ ├── grid2.png │ ├── grid20.png │ ├── grid3.png │ ├── grid4.png │ ├── grid5.png │ ├── grid6.png │ ├── grid7.png │ ├── grid8.png │ └── grid9.png │ ├── index.html │ ├── js │ ├── base.js │ ├── bootstrap-3.0.3.min.js │ ├── highlight.pack.js │ └── jquery-1.10.2.min.js │ ├── mkdocs │ ├── js │ │ ├── lunr.min.js │ │ ├── mustache.min.js │ │ ├── require.js │ │ ├── search-results-template.mustache │ │ ├── search.js │ │ └── text.js │ └── search_index.json │ └── sitemap.xml ├── requirements.txt └── source ├── _static └── img │ ├── appendix │ └── practice │ │ ├── image1.png │ │ └── image2.png │ ├── appendix_a2_1.png │ ├── appendix_a2_2.png │ ├── appendix_a5_1.png │ ├── appendix_a5_2.png │ ├── chapter_02 │ └── Rplot.png │ ├── chapter_05 │ ├── appendix_a5_1.png │ └── appendix_a5_2.png │ ├── circos-anatomy.png │ ├── fork.png │ ├── miseq.jpg │ ├── pull_request.png │ └── ubuntu.jpg ├── appendix ├── edirect.rst ├── file_format.rst ├── get_data.rst ├── index.rst ├── introduce_lab.rst └── practice.rst ├── chapter_00 ├── Aspera_Connect.rst ├── FastQC.rst ├── RAxML.rst ├── SPAdes.rst └── index.rst ├── chapter_01 ├── 01_get_data.rst ├── 02_quality_control.rst ├── 03_assembly.rst ├── 04_annotation.rst ├── 05_practice.rst └── index.rst ├── chapter_02 ├── 01_blast.rst ├── 02_msa.rst ├── 03_mapping.rst ├── 04_call_variant.rst └── index.rst ├── chapter_03 ├── 01_pangenomics.rst ├── 02_orthologs_analysis.rst ├── 03_phylogenomics.rst ├── 04_get_homologues.rst ├── aln2phy.py ├── index.rst ├── realphy.docker └── snp.rst ├── chapter_04 ├── 01_circos.rst ├── 02_ggplot2.rst ├── 03_genome_viewer.rst └── index.rst ├── chapter_05 ├── 01_cloud.rst ├── 02_aws.rst ├── 03_docker.rst ├── 04_galaxy.rst └── index.rst ├── chapter_06 ├── 01_metagenomics.rst ├── 02_centrifuge.rst ├── 03_clark-s.rst ├── 04_kraken.rst ├── 05_meta-beetl.rst └── index.rst ├── chapter_07 ├── 01_snippy.rst ├── 02_realphy.rst ├── 03_ksnp.rst ├── 04_snp-pipeline.rst └── index.rst ├── chapter_08 ├── 01_mummer.rst ├── 02_mauve.rst └── index.rst ├── conf.py ├── index.rst └── preface ├── 01_linux.rst ├── 02_shell.rst ├── 03_python.rst ├── 04_perl.rst ├── 05_awk.rst ├── 06_sed.rst ├── 07_r.rst ├── 08_docker.rst ├── 09_git.rst ├── 10_ngs_basic.rst ├── 11_resource.rst └── index.rst /.Rhistory: 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