A 3 day microbial bioinformatics workshop conducted by Dr. Evan Snitkin at University of Michigan. This module covers the basics of microbial genomic analysis using publicly available tools that are commonly referenced in genomics literature. Students will learn the steps and associated tools that are required to process, annotate and compare microbial genomes.

Date: Feb 28 - 2 March 2018

• Prior participation in a Software Carpentry Workshop

GOTO: http://comparative-genomics.readthedocs.io/en/latest/index.html#

Day 1 Morning

• Installing and setting up Cyberduck for file transfer
• Getting your data onto Flux and setting up Environment variable
• Unix is your friend
• Quality Control using FastQC
• Quality Trimming using Trimmomatic

Day 1 Afternoon

• Read Mapping
• Variant Calling
• Visualize BAM/VCF files in Artemis
• VRE variant calling analysis

Day 2 Morning

• Genome Assembly
• Assembly evaluation
• Compare assembly to reference genome and Post-assembly genome improvement
• Map reads to the final ordered assembly
• Genome Annotation

Day 2 Afternoon

• Determine which genomes contain beta-lactamase genes
• Identification of antibiotic resistance genes with ARIBA directly from paired-end reads
• Perform pan-genome analysis with Roary

Day 3 Morning

• Perform whole genome alignment with Mauve
• Perform DNA sequence comparisons and phylogenetic analysis in ape
• Perform SNP density analysis to discern evidence of recombination
• Perform recombination filtering with gubbins
• Create annotated publication quality trees with iTOL

Day 3 Afternoon

• Perform QC on fastq files
• Examine results of SPANDx pipeline
• Recombination detection and tree generation
• Phylogenetic tree annotation and visualization
• Assessment of genomic deletions

Helpful resources for microbial genomics