Metagenomics: Intro to Whole Shotgun Metagenomic Sequencing (Part 4 of 4)

Adelaide Rhodes, Senior Bioinformatics Scientist, will be presenting an overview of shotgun metagenomic sequencing data analysis using the Tufts High Performance Computing Cluster. 

Metagenomics has two main types of analysis: Metabarcoding and Whole Genome Shotgun Sequencing. Metabarcoding (or amplicon-based sequences focuses on taxonomically describing species within a sample from a subset of the genome, usually the highly conserved and phylogenetically informative ribosomal sequences (16S, 18S, 23S) or internal transcribed spacers (ITS). Metabarcoding infers function from the taxonomic composition, whereas whole shotgun sequencing metagenomics involves using data derived from all the genomic data and ascribes function based on the detection of coding sequences.

This virtual workshop is part three of a four part series and will focus on command line tools and best practices for building a bioinformatics workflow for genome-resolved metagenomic data analysis. We will explore tools involved in a typical workflow similar to Metawrap as well as output visualizations using BlobTools.

https://github.com/bxlab/metaWRAP

https://github.com/DRL/blobtools

Prerequisites:

Because we are covering advanced material in this session using Tufts HPC and RStudio, attendees are expected to either have:

1. Proficiency with HPC or attended an Intro to HPC/Slurm For Life Sciences (October 19) or equivalent

2. Proficiency with RStudio or attended Intro to RStudio For Life Sciences (October 26) or equivalent

3. All attendees will need an HPC cluster account. Please use the following link to create an account if you do not already have one:  HPC Cluster Account Request Form

In order to allow time for account creation, workshop registration will close one week in advance, October 26th.

Please email bioinformatics-workshop-questions@elist.tufts.edu with questions about this workshop.

This workshop is part of a series being offered in Fall, 2022 to the Tufts Community.

Part I: October 19th  - Intro to HPC/Slurm/Linux for Life Sciences 

Part II: October 26th - Intro to RStudio for Life Sciences

Part III: November 2nd - Metagenomics I: Intro to 16 Metabarcoding

Part IV: November 9th - Intro to Whole Shotgun Metagenomic Sequencing  - this workshop