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
- Prior participation in a Data Carpentry Workshop
The Workshop directory on Great Lakes that you will be working in is - /scratch/micro612w21_class_root/micro612w21_class/
You can find a folder named after your username/uniqname; for example if my uniqname is apirani, I will be working in /scratch/micro612w21_class_root/micro612w21_class/apirani This would be the directory that workshop attendees will be working from.
A Read the Docs technical documentation is available for the workshop's README text that will display an index to its left for faster access. However, this website will not be updated during workshop hours. To access the website, use the link below
https://comparative-genomics.readthedocs.io/en/latest/index.html
- Installing and setting up Cyberduck for file transfer
- Getting your data onto Flux and setting up Environment variable
- Unix is your friend
- Submit Variant Calling Job
- Contamination Screening using Kraken
- Quality Control using FastQC
- Quality Trimming using Trimmomatic
- Read Mapping
- Variant Calling
- Visualize BAM/VCF files in Artemis
- Exercise: Daptomycin resistance in VRE
- Exercise: Colistin resistance in Acinetobacter
- Genome Assembly
- Assembly evaluation
- Compare assembly to reference genome and Post-assembly genome improvement
- Genome Annotation
- Determine which genomes contain KPC genes using BLAST
- Identify antibiotic resistance genes with ARIBA directly from paired end reads
- Perform pan-genome analysis with Roary
- Perform whole genome alignment with Parsnp
- Perform DNA sequence comparisons and phylogenetic analysis in ape
- Perform SNP density analysis to discern evidence of recombination
- Perform recombination filtering with gubbins
- Overlay metadata on your tree using R
- Perform QC on fastq files
- Run ARIBA CARD and MLST typing on day3pm_fastq samples
- Examine results of Snippy pipeline
- Recombination detection and tree generation
- Phylogenetic tree annotation and visualization
Helpful resources for microbial genomics