Welcome to Microbial Genomics Lab Spring 2022¶
Contents:
- Introduction
- Week 1
- Setting up your computing environment
- Unix and commandline environment
- Install and configure Miniconda and Bioconda
- Git and Github
- Install Jupyter and Jupyter-lab
- Tools to install for next week
- Week 2
- A brief introduction to
pandoc - Alternative ways to convert Markdown files to PDF
- Brief introduction to Markdown
- Text
- Install tools for today’s lab
- Exercises for today
- Week 3
- Genome Assembly using SPAdes
- Introduction to SPAdes
- Installing SPAdes
- Running SPAdes
- Checking sequence qualities
- Trimming the sequences
- Run fastqc on quality-trimmed sequences to compare its quality with untrimmed sequences
- Running the assembly on your laptop or home computer
- Running the assembly on a cluster at GW
- Checking the quality of assemblies
- Test trimming parameters and run another SPAdes assembly
- Cluster login info
- Week 4
- Exercises for Week4
- Virtual environments in Python
- Connecting to GW HPC cluster (Cerberus)
- Using ssh keys to log in to
cerberus - File and folder organization on
cerberus - Transferring files to/from
cerberus - Installation of Miniconda and Bioconda on
cerberus - File transfer between computers using
rsync - Submitting jobs on
cerberus - Checking assembly results
- Viewing assemblies with Bandage
- Transfer metagenomic data to
cerberusfor next week
- Week 5
- Exercises for Week 5
- Recap job submission on Cerberus
- Install tools needed for today’s exercises
- Run metagenome assemblies on
cerberus - Checking assembly metrics using Quast
- Download data for unicycler assembly
- Run unicycler assembly on cerberus
- Run Metabat2 on your own after class
- Run CheckM on your own after class
- Run RefineM on your own after class
- Going further
- Things for you to find out after you complete the exercises
- Week 6
- Compuational Exercises
- Go over last week’s results
- Identification of 16S rRNA genes in MAGs
- Running BLAST to identify the MAGs with 16S genes
- Running Web-based BLAST searches
- Install GTDB-TK on Cerberus
- Test run GTDB-TK on Cerberus
- Web-based GTDB-TK on KBase
- Retrieve related sequences to construct a phylogeny
- Construct a simple phylogenetic tree
- Viewing the phylogenetic tree
- Week 7
- Computational Exercises
- Week 9
- Computational Lab Exercises
- Run fastANI to compare genomes
- Anvi’o
- Week 10
- Computational lab exercises
- Install R and RStudio
- Start RStudio and install required packages
- Some resources for learning R
- Install reference data files needed to run DADA2
- Run an example dataset using DADA2 tutorial
- Run DADA2 on 16S amplicon data from publicly available datasets
- Documenting your workflow in R
- Some important terminology for you to learn and remember
- Week 11
- Introduction to Python programming
- Week 12
- Visualization of microbial genomes
- Visualization of gene segments or clusters
- Phylogenetic trees visualization
- Final comments
