Summary and Setup

Welcome to the Genome Assembly Workshop

This workshop provides a hands-on introduction to long-read genome assembly using HiFiasm and Flye, optimized for the RCAC cluster. You’ll learn best practices for assembly, polishing, and scaffolding with Bionano optical maps, along with strategies for quality assessment and troubleshooting.

Designed for researchers and bioinformaticians, this workshop will equip you with the skills to build high-quality, reproducible genome assemblies on RCAC HPC resources.

Let’s get started!

Instructors

  1. Arun Seetharam, Ph.D.: Arun is a lead bioinformatics scientist at Purdue University’s Rosen Center for Advanced Computing. With extensive expertise in comparative genomics, genome assembly, annotation, single-cell genomics, NGS data analysis, metagenomics, proteomics, and metabolomics. Arun supports a diverse range of bioinformatics projects across various organisms, including human model systems.

Schedule

Time Session
9:00 AM Introduction to Genome Assembly – Sequencing technologies, assembly concepts, and workshop overview
9:30 AM Assembly Strategies – Comparing approaches, evaluation metrics, and resource planning
9:50 AM Data Quality Control – NanoPlot, Filtlong, KMC, and GenomeScope2 for read QC
10:30 AM Morning Break
10:45 AM PacBio HiFi Assembly – HiFiasm assembly, purge levels, GFA conversion, and Flye for HiFi
12:00 PM Lunch Break
1:00 PM Oxford Nanopore Assembly – Flye assembler, Medaka polishing, and HiFiasm for ONT
1:45 PM Hybrid Assembly – Combining ONT + HiFi reads with Flye, Bionano scaffolding
2:30 PM Afternoon Break
2:45 PM Scaffolding with Optical Genome Mapping – Bionano Solve for HiFiasm and Flye assemblies
3:15 PM Assembly Evaluation – QUAST, Compleasm, Merqury, Bandage, and comparative analysis
3:50 PM Wrap-Up & Discussion – Summary, Q&A, and next steps
4:00 PM Dismissal

What is not covered

  1. Short read assembly
  2. Hi-C scaffolding
  3. Annotation
  4. Comparative analyses

Pre-requisites

  1. Basic knowledge of genomics
  2. Basic knowledge of command line interface
  3. Basic knowledge of bioinformatics tools

Data Sets

To copy the data to your scratch space:

BASH 

rsync -avP /depot/workshop/data/genome-assembly/genome-assembly-data $RCAC_SCRATCH

The worked-out results folder is also available at /depot/workshop/data/genome-assembly/genome-assembly-data on the training cluster. Only use this if you are unable to finish the exercises in the workshop.

Software Setup

Discussion

Details

SSH key setup for different systems is detailed in the expandable sections below.

Open a terminal and run:

SH 

ssh-keygen -b 4096 -t rsa
type .ssh\id_rsa.pub | ssh trainXX@negishi.rcac.purdue.edu "mkdir -p ~/.ssh; cat >> ~/.ssh/authorized_keys"

Open Terminal and run

SH 

ssh-keygen -b 4096 -t rsa
cat .ssh/id_rsa.pub | ssh trainXX@negishi.rcac.purdue.edu "mkdir -p ~/.ssh; cat >> ~/.ssh/authorized_keys"

Open a terminal and run:

SH 

ssh-keygen -b 4096 -t rsa
cat .ssh/id_rsa.pub | ssh trainXX@negishi.rcac.purdue.edu "mkdir -p ~/.ssh; cat >> ~/.ssh/authorized_keys"