├── .idea ├── .name ├── Comparative_Genomics.iml ├── dictionaries │ └── alipirani.xml ├── encodings.xml ├── libraries │ └── R_User_Library.xml ├── misc.xml ├── modules.xml ├── scopes │ └── scope_settings.xml ├── vcs.xml └── workspace.xml ├── Micro612_pre-course_hw ├── Micro612_w17_pre-course_hw.pdf ├── Micro612_w18_pre-course_hw.pdf ├── Micro612_w21_pre-course_hw.docx └── README.md ├── Presentation_slides ├── 2016-3-25_lecture_slides.pdf ├── 2021-04-21_lecture_slides.pdf ├── Intro To Cluster Computing Micro612 W2021.pdf └── IntroToClusterComputingMicro612Winter2016.pdf ├── README.md ├── _img ├── README.md ├── day1_after │ ├── 1_1.png │ ├── HET_variant.png │ ├── HET_variant_gene_selected.png │ ├── IGV_FQ.png │ ├── IGV_true_error.png │ ├── artemis │ │ ├── HET_variant.png │ │ ├── HET_variant_gene_selected.png │ │ ├── graphs.png │ │ ├── read_details.png │ │ ├── select_graph.png │ │ └── spike_true.png │ ├── graphs.png │ ├── igv_het.png │ ├── igv_mgrb.png │ ├── igv_zoomed_in1.png │ ├── igv_zoomed_in2.png │ ├── igv_zoomed_in3.png │ ├── igv_zoomed_in4.png │ ├── igv_zoomed_out.png │ ├── picard.png │ ├── read_details.png │ ├── select_graph.png │ └── spike_true.png ├── day1_morning │ ├── 1.png │ ├── 2.png │ ├── 3.png │ ├── plot_1.png │ ├── plot_2.png │ └── trimm_parameters.png ├── day2_after │ └── lsbsr.pngh ├── day2_morning │ ├── aligned_reads_deletion.png │ ├── beautiful.png │ ├── beautiful_old.png │ ├── day2_morn_mecA.png │ ├── intro.png │ ├── mess.png │ └── multiqc.jpeg └── spandx.jpg ├── backup ├── README.md └── sed.sh ├── copy.sh ├── day1_afternoon ├── README.md ├── detailed_var_call.png ├── genomics_pipeline.png ├── genomics_pipeline_qc.png ├── genomics_pipeline_variant_calling.png └── variant_annot.png ├── day1_morning └── README.md ├── day2_afternoon ├── README.md ├── comp_genomics.png ├── comp_genomics_details_ACT.png ├── comp_genomics_details_blast.png └── comp_genomics_details_roary.png ├── day2_morning ├── README.md ├── annotation_details_ACT.png ├── annotation_details_prokka.png ├── assembly_details_abacas.png ├── assembly_details_quast.png ├── assembly_details_spades.png ├── genome_annotation.png └── genome_assembly.png ├── day3_afternoon └── README.md ├── day3_morning ├── README.md └── phylo.png ├── docs ├── Makefile ├── build │ ├── doctrees │ │ ├── day1_afternoon.doctree │ │ ├── day1_morning.doctree │ │ ├── day2_afternoon.doctree │ │ ├── day2_morning.doctree │ │ ├── day3_afternoon.doctree │ │ ├── day3_morning.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── index_backup.doctree │ │ ├── index_temp.doctree │ │ ├── online_resources.doctree │ │ └── test.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ ├── 1.png │ │ ├── 1_1.png │ │ ├── 2.png │ │ ├── 3.png │ │ ├── HET_variant.png │ │ ├── HET_variant_gene_selected.png │ │ ├── aligned_reads_deletion.png │ │ ├── beautiful.png │ │ ├── graphs.png │ │ ├── igv_het.png │ │ ├── igv_mgrb.png │ │ ├── igv_zoomed_in1.png │ │ ├── igv_zoomed_in2.png │ │ ├── igv_zoomed_in3.png │ │ ├── igv_zoomed_in4.png │ │ ├── igv_zoomed_out.png │ │ ├── intro.png │ │ ├── multiqc.jpeg │ │ ├── picard.png │ │ ├── plot_1.png │ │ ├── plot_2.png │ │ ├── read_details.png │ │ ├── select_graph.png │ │ ├── spandx.jpg │ │ ├── spike_true.png │ │ └── trimm_parameters.png │ │ ├── _sources │ │ ├── day1_afternoon.txt │ │ ├── day1_morning.txt │ │ ├── day2_afternoon.txt │ │ ├── day2_morning.txt │ │ ├── day3_afternoon.txt │ │ ├── day3_morning.txt │ │ ├── index.rst.txt │ │ ├── index.txt │ │ ├── index_backup.txt │ │ ├── index_temp.txt │ │ ├── online_resources.txt │ │ └── test.txt │ │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ └── fontawesome-webfont.woff │ │ ├── jquery-1.11.1.js │ │ ├── jquery-3.1.0.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── day1_afternoon.html │ │ ├── day1_morning.html │ │ ├── day2_afternoon.html │ │ ├── day2_morning.html │ │ ├── day3_afternoon.html │ │ ├── day3_morning.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── index_backup.html │ │ ├── index_temp.html │ │ ├── objects.inv │ │ ├── online_resources.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── test.html ├── make.bat └── source │ ├── 1.png │ ├── 1_1.png │ ├── 2.png │ ├── 3.png │ ├── HET_variant.png │ ├── HET_variant_gene_selected.png │ ├── IGV_FQ.png │ ├── IGV_true_error.png │ ├── aligned_reads_deletion.png │ ├── beautiful.png │ ├── conf.py │ ├── copy.sh │ ├── day1_afternoon.md │ ├── day1_morning.md │ ├── day2_afternoon.md │ ├── day2_morn_mecA.png │ ├── day2_morning.md │ ├── day3_afternoon.md │ ├── day3_morning.md │ ├── graphs.png │ ├── igv_het.png │ ├── igv_mgrb.png │ ├── igv_zoomed_in1.png │ ├── igv_zoomed_in2.png │ ├── igv_zoomed_in3.png │ ├── igv_zoomed_in4.png │ ├── igv_zoomed_out.png │ ├── index.rst │ ├── index_backup.md │ ├── intro.png │ ├── mess.png │ ├── multiqc.jpeg │ ├── online_resources.md │ ├── picard.png │ ├── plot_1.png │ ├── plot_2.png │ ├── read_details.png │ ├── sed.sh │ ├── sed_image.sh │ ├── select_graph.png │ ├── spandx.jpg │ ├── spike_true.png │ └── trimm_parameters.png ├── online_resources └── README.md └── spandx.jpg /.idea/.name: -------------------------------------------------------------------------------- 1 | Comparative_Genomics 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