├── .gitignore ├── 0.01-intro.Rmd ├── 0.02-eric-notes.Rmd ├── 1.00-essential-computing-overview.Rmd ├── 1.01-unix.Rmd ├── 1.015-shell-programming.Rmd ├── 1.02-sed-awk-regex.Rmd ├── 1.030-working-on-remote-servers.Rmd ├── 1.035-hpc.Rmd ├── 2.00-rep-res-intro.Rmd ├── 2.01-rstudio-prj-org.Rmd ├── 2.02-version-control.Rmd ├── 2.03-tidyverse.Rmd ├── 2.04-Rmd-notebooks-etc.Rmd ├── 2.05-managing-workflows-with-snakemake.Rmd ├── 3.00-bioinfo-intro.Rmd ├── 3.01-ngs-data-acquisition.Rmd ├── 3.02-bioinf-file-formats.Rmd ├── 3.03-genome-assembly.Rmd ├── 3.04-sequence-alignment.Rmd ├── 3.05-variant-calling.Rmd ├── 3.05.5-basic-handling-of-VCF-files.Rmd ├── 3.06-RAD-w-and-wo-a-reference.Rmd ├── 3.07-amplicon-seq.Rmd ├── 3.08-annotation-stuff.Rmd ├── 3.10-whole-genome-alignment.Rmd ├── 3.12-an-example-full-WGS-workflow.Rmd ├── 4.00-post-variant-intro.Rmd ├── 5.00-pop-gen-intro.Rmd ├── 9-references.Rmd ├── LICENSE ├── README.md ├── _bookdown.yml ├── _output.yml ├── apalike.bst ├── book.bib ├── chains.pdf ├── chapter_review_inputs └── unix-chapter-review-terms.txt ├── css └── style.css ├── docs ├── 404.html ├── a-fast-furious-overview-of-the-tidyverse.html ├── alignment-of-sequence-data-to-a-reference-genome-and-associated-steps.html ├── an-example-full-workflow-from-sequences-to-variants.html ├── authoring-reproducibly-with-rmarkdown.html ├── basic-handling-of-vcf-files.html ├── bioinformatic-analysis-on-variant-data.html ├── bioinformatic-file-formats.html ├── bioinformatics-for-rad-seq-data-with-and-without-a-reference-genome.html ├── boneyard-1.html ├── chap-HPCC.html ├── css │ └── style.css ├── dna-sequences-and-sequencing.html ├── downloads │ ├── CH_plate1_A01_mkdup-100-lines.sam │ ├── CH_plate1_A01_mkdup.bam │ ├── WP.pgchr1_10K.genotype.gz │ ├── gbs-miscall.pdf │ ├── genotype.readme │ ├── pearl_millet_v1.1.fa.fai │ └── s001---1.sam ├── eca-bioinf-handbook.epub ├── eca-bioinf-handbook.pdf ├── eca-bioinf-handbook.tex ├── eca-bioinf-handbook_files │ └── figure-html │ │ ├── sanger-1.png │ │ ├── sanger2-1.png │ │ ├── unnamed-chunk-76-1.png │ │ ├── unnamed-chunk-77-1.png │ │ ├── unnamed-chunk-78-1.png │ │ ├── unnamed-chunk-82-1.png │ │ ├── unnamed-chunk-83-1.png │ │ └── unnamed-chunk-84-1.png ├── erics-notes-of-what-he-might-do.html ├── essential-unixlinux-terminal-knowledge.html ├── example-wgs-flow.html ├── figs │ ├── DNA_chemical_structure.svg │ ├── DNA_chemical_structure_2.svg │ ├── ascii-crop.png │ ├── base-0-and-1-cropped.svg │ ├── crick-and-watson.png │ ├── file-hierarchy.png │ ├── filezilla-connected.png │ ├── filezilla-connection-timeout.png │ ├── filezilla-password.png │ ├── filezilla-site.png │ ├── full-geno-like-dag.svg │ ├── genotypes_and_reads.svg │ ├── git-staged.png │ ├── git-window.png │ ├── globus1.png │ ├── globus10.png │ ├── globus11.png │ ├── globus2.png │ ├── globus3.png │ ├── globus4.png │ ├── globus5.png │ ├── globus6.png │ ├── globus7.png │ ├── globus8.png │ ├── globus9.png │ ├── haplotype-caller-run-times.svg │ ├── iterm-pw-trigger.png │ ├── pcr-duplicates.svg │ ├── permissions.png │ ├── plated-single-geno-like.svg │ ├── quickie.jpg │ ├── single-geno-like.svg │ ├── snakemake-dags │ │ ├── bwa-map.svg │ │ ├── fastqc-multiqc.svg │ │ ├── full-dag.svg │ │ ├── genomics-db-import.svg │ │ ├── genomics-db2vcf.svg │ │ ├── make-gvcfs.svg │ │ ├── mark-dup.svg │ │ ├── merge-lib-samp.svg │ │ └── trimmo.svg │ ├── summit-tmux-add-trigger.png │ ├── summit-tmux-command.png │ ├── summit-tmux-new-profile.png │ ├── summit-tmux-trigger-setup.png │ ├── summit-tmux-triggers.png │ ├── tmux-4-panes.png │ └── wildcard_propagation_1.svg ├── genome-annotation.html ├── genome-assembly.html ├── handle-vcf.html ├── high-performance-computing-clusters-hpccs.html ├── images │ ├── caution.png │ ├── important.png │ ├── note.png │ ├── tip.png │ └── warning.png ├── index.html ├── intro.html ├── introduction-to-reproducible-research.html ├── libs │ ├── accessible-code-block-0.0.1 │ │ └── empty-anchor.js │ ├── accessible-code-block │ │ └── empty-anchor.js │ ├── anchor-sections-1.0.1 │ │ ├── anchor-sections.css │ │ └── anchor-sections.js │ ├── anchor-sections-1.1.0 │ │ ├── anchor-sections-hash.css │ │ ├── anchor-sections.css │ │ └── anchor-sections.js │ ├── anchor-sections │ │ ├── anchor-sections-hash.css │ │ ├── anchor-sections.css │ │ └── anchor-sections.js │ ├── gitbook-2.6.7 │ │ ├── css │ │ │ ├── fontawesome │ │ │ │ └── fontawesome-webfont.ttf │ │ │ ├── plugin-bookdown.css │ │ │ ├── plugin-clipboard.css │ │ │ ├── plugin-fontsettings.css │ │ │ ├── plugin-highlight.css │ │ │ ├── plugin-search.css │ │ │ ├── plugin-table.css │ │ │ └── style.css │ │ └── js │ │ │ ├── app.min.js │ │ │ ├── clipboard.min.js │ │ │ ├── jquery.highlight.js │ │ │ ├── lunr.js │ │ │ ├── plugin-bookdown.js │ │ │ ├── plugin-clipboard.js │ │ │ ├── plugin-fontsettings.js │ │ │ ├── plugin-search.js │ │ │ └── plugin-sharing.js │ ├── gitbook │ │ ├── css │ │ │ ├── fontawesome │ │ │ │ └── fontawesome-webfont.ttf │ │ │ ├── plugin-bookdown.css │ │ │ ├── plugin-clipboard.css │ │ │ ├── plugin-fontsettings.css │ │ │ ├── plugin-highlight.css │ │ │ ├── plugin-search.css │ │ │ ├── plugin-table.css │ │ │ └── style.css │ │ └── js │ │ │ ├── app.min.js │ │ │ ├── clipboard.min.js │ │ │ ├── jquery.highlight.js │ │ │ ├── lunr.js │ │ │ ├── plugin-bookdown.js │ │ │ ├── plugin-clipboard.js │ │ │ ├── plugin-fontsettings.js │ │ │ ├── plugin-search.js │ │ │ └── plugin-sharing.js │ ├── header-attrs-2.11 │ │ └── header-attrs.js │ ├── header-attrs │ │ └── header-attrs.js │ ├── jquery-2.2.3 │ │ └── jquery.min.js │ ├── jquery-3.6.0 │ │ └── jquery-3.6.0.min.js │ └── jquery │ │ ├── jquery-3.6.0.min.js │ │ └── jquery.min.js ├── managing-workflows-with-snakemake.html ├── overview-of-bioinformatic-analyses.html ├── overview-of-essential-computing-skills.html ├── processing-amplicon-sequencing-data.html ├── reference-keys.txt ├── references-1.html ├── rstudio-and-project-centered-organization.html ├── search_index.json ├── sed-awk-and-regular-expressions.html ├── shell-programming.html ├── snakemake-chap.html ├── topics-in-pop-gen.html ├── using-python.html ├── variant-annotation.html ├── variant-calling.html ├── version-control.html ├── whole-genome-alignment-strategies.html └── working-on-remote-servers.html ├── eca-bioinf-handbook.Rproj ├── figs ├── DNA_chemical_structure.pdf ├── DNA_chemical_structure.svg ├── DNA_chemical_structure_2.pdf ├── DNA_chemical_structure_2.svg ├── ascii-crop.pdf ├── ascii-crop.png ├── base-0-and-1-cropped.svg ├── crick-and-watson.pdf ├── crick-and-watson.png ├── file-hierarchy.pdf ├── file-hierarchy.png ├── filezilla-connected.png ├── filezilla-connection-timeout.png ├── filezilla-password.png ├── filezilla-site.png ├── full-geno-like-dag.pdf ├── full-geno-like-dag.svg ├── genotypes_and_reads.pdf ├── genotypes_and_reads.svg ├── git-staged.pdf ├── git-staged.png ├── git-window.pdf ├── git-window.png ├── globus1.png ├── globus10.png ├── globus11.png ├── globus2.png ├── globus3.png ├── globus4.png ├── globus5.png ├── globus6.png ├── globus7.png ├── globus8.png ├── globus9.png ├── haplotype-caller-run-times.svg ├── ident-99.5.chin_nc_chroms_v_coho1.pdf ├── iterm-pw-trigger.png ├── pcr-duplicates.pdf ├── pcr-duplicates.svg ├── permissions.pdf ├── permissions.png ├── plated-single-geno-like.pdf ├── plated-single-geno-like.svg ├── quickie.jpg ├── single-geno-like.pdf ├── single-geno-like.svg ├── snakemake-dags │ ├── bwa-map.svg │ ├── fastqc-multiqc.svg │ ├── full-dag.svg │ ├── genomics-db-import.svg │ ├── genomics-db2vcf.svg │ ├── make-gvcfs.svg │ ├── mark-dup.svg │ ├── merge-lib-samp.svg │ └── trimmo.svg ├── summit-tmux-add-trigger.png ├── summit-tmux-command.png ├── summit-tmux-new-profile.png ├── summit-tmux-trigger-setup.png ├── summit-tmux-triggers.png ├── tmux-4-panes.pdf ├── tmux-4-panes.png └── wildcard_propagation_1.svg ├── figure-creation ├── 1.01-unix │ ├── .gitignore │ ├── file-hierarchy.dot │ └── file-hierarchy.sh ├── base-1-beads-and-0-fences │ ├── Untitled.R │ └── base-0-and-1.svg ├── genotype-likelihood-dag │ ├── full-geno-like-dag.svg │ ├── genos-and-reads-dag.svg │ ├── plated-single-geno-like.svg │ └── single-geno-like.svg ├── haplotype-caller-run-times │ ├── hc-times-plot.R │ └── hc_times.csv ├── non-model-wgs-workflow-dags │ ├── bwa-map.dot │ ├── fastqc-multiqc.dot │ ├── full-dag.dot │ ├── genomics-db-import.dot │ ├── genomics-db2vcf.dot │ ├── gray-dag.dot │ ├── make-gvcfs.dot │ ├── mark-dup.dot │ └── trimmo.dot └── snakemake-wildcards │ ├── snakefile1.png │ └── wildcard_propagation_1.svg ├── images ├── caution.png ├── important.png ├── note.png ├── tip.png └── warning.png ├── index.Rmd ├── inputs ├── chain-chinook1_vs_coho10.rdp.gz ├── chin28_vs_coho28.rdp.gz ├── chin_nc_vs_coho1-chain.rdp.gz └── chinook1_vs_coho10.rdp.gz ├── krantz.cls ├── latex ├── after_body.tex └── before_body.tex ├── references.bib └── table_inputs ├── metachars.txt ├── minimal-tmux.txt ├── module_subcommands.txt ├── sam-columns-table.txt ├── sam-flag-table.txt ├── 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