A 3 day microbial bioinformatics workshop conducted by Dr. Evan Snitkin at University of Michigan
Date: 28 - 30 March
Link to Software Carpentry Etherpad: http://pad.software-carpentry.org/micro612_bacterial_genomics_workshop
- [Getting your data onto Flux and setting up Environment variable](https://github.com/alipirani88/Comparative_Genomics/blob/master/day1_morning/README.md#getting-your-data-onto-glux-and-setting-up-environment-variable)
- [Quality Control using FastQC](https://github.com/alipirani88/Comparative_Genomics/blob/master/day1_morning/README.md#quality-control-using-fastqc)
- [Quality Trimming using Trimmomatic](https://github.com/alipirani88/Comparative_Genomics/blob/master/day1_morning/README.md#quality-trimming-using-trimmomatic)
- [Read Mapping](https://github.com/alipirani88/Comparative_Genomics/blob/master/day1_afternoon/README.md#read-mapping)
- [Variant Calling](https://github.com/alipirani88/Comparative_Genomics/blob/master/day1_afternoon/README.md#variant-calling-and-filteration)
- [Visualize BAM/VCF files in Artemis](https://github.com/alipirani88/Comparative_Genomics/blob/master/day1_afternoon/README.md#visualize-bam-and-vcf-files-in-artemis)
- [Genome Assembly](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_morning/README.md#genome-assembly)
- [Assembly evaluation](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_morning/README.md#assembly-evaluation-using-quast)
- [Compare assembly to reference genome and Post-assembly genome improvement](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_morning/README.md#compare-assembly-to-reference-genome-and-post-assembly-genome-improvement)
- [Map reads to the final ordered assembly](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_morning/README.md#map-reads-to-the-final-ordered-assembly)
- [Genome Annotation](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_morning/README.md#genome-annotation)
- [Determine which genomes contain beta-lactamase genes](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_afternoon/README.md#determine-which-genomes-contain-beta-lactamase-genes)
- [Identification of antibiotic resistance genes with LS-BSR and the ARDB database](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_afternoon/README.md#identification-of-antibiotic-resistance-genes-with-ls-bsr-and-the-ardb-database)
- [Perform pan-genome analysis with LS-BSR](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_afternoon/README.md#perform-pan-genome-analysis-with-ls-bsr)
- [Perform genome comparisons with ACT](https://github.com/alipirani88/Comparative_Genomics/blob/master/day2_afternoon/README.md#perform-genome-comparisons-with-act)
- [Perform whole genome alignment with Mauve](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_morning/README.md#perform-whole-genome-alignment-with-Mauve)
- [Perform DNA sequence comparisons and phylogenetic analysis in ape](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_morning/README.md#perform-some-dna-sequence-comparisons-and-phylogenetic-analysis-in-ape)
- [Perform SNP density analysis to discern evidence of recombination](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_morning/README.md#perform-snp-density-analysis-to-discern-evidence-of-recombination)
- [Perform recombination filtering with gubbins](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_morning/README.md#perform-recombination-filtering-with-gubbins)
- [Create annotated publication quality trees with iTOL](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_morning/README.md#create-annotated-publication-quality-trees-with-itol)
- [Perform QC on fastq files](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_afternoon/README.md#perform-qc-on-fastq-files)
- [Examine results of SPANDx pipeline](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_afternoon/README.md#examine-results-of-spandx-pipeline)
- [Recombination detection and tree generation](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_afternoon/README.md#recombination-detection-and-tree-generation)
- [Phylogenetic tree annotation and visualization](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_afternoon/README.md#phylogenetic-tree-annotation-and-visualization)
- [Assessment of genomic deletions](https://github.com/alipirani88/Comparative_Genomics/blob/master/day3_afternoon/README.md#assessment-of-genomic-deletions)