Microbial Comparative Genomics Workshop - 2021¶
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: April 21 - 23 2021
Prerequisites¶
Prior participation in a Data Carpentry Workshop
Workshop¶
- Day 1 Morning
- Day 1 Afternoon
- Goal
- Overview of Genomics Pipeline
- Contamination Screening using Kraken
- Quality Control using FastQC
- Quality Trimming using Trimmomatic
- Variant Calling for Collistin resistant Klebsiella pneumoniae
- Step1_cleaning
- Step2_mapping
- Step3_samtobamconversion
- Step4_removeduplicates
- Step5_variantcalling
- Step6_variantfilteraion
- Step 7 bgzip and Tabix index vcf files for IGV visualization.
- Variant Annotation using snpEff
- Generate Alignment Statistics
- Visualize BAM and VCF files in IGV (Integrative Genome Viewer)
- Exercise: Daptomycin resistance in VRE
- Exercise: Colistin resistance in Acinetobacter
- Day 2 Morning
- Goal
- Genome Assembly using Spades Pipeline
- Submit PROKKA annotation job
- Assembly evaluation using QUAST
- Generating multiple sample reports using multiqc
- Compare assembly to reference genome and post-assembly genome improvement
- Genome Annotation
- Using abacas and ACT to compare VRE/VSE genome
- Prep for this afternoon
- Day 2 Afternoon
- Day 3 Morning
- Goal
- Perform Whole genome alignment with Parsnp and convert alignment to other useful formats
- Perform some DNA sequence comparisons and phylogenetic analysis in APE, an R package
- Perform SNP density analysis to discern evidence of recombination
- Perform recombination filtering with Gubbins
- Overlay metadata on your tree using R
- Day 3 Afternoon
- Helpful resources for microbial genomics