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      Genome Assembly Workshop 2020

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
Genome Assembly
Introduction to the DNA Tech Core
A Brief Overview of Genome Annotation, with a Focus on the Use of Isoseq
Support
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
Conda
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (extra)
Snakemake
Introduction
Challenge Answers
K-mers
K-mers tutorial
PacBio
Introduction to PacBio HiFi Data and Applications
Genome Assembly with PacBio HiFi Data
Improved Phased Assembly (IPA) Using HiFi Data
Assembling the drosophila genome with IPA and HiFi data
ONT Assembly
Introduction to ONT
Assembly using ONT - Hands-on
Bionano
Optical mapping for accurate genome assembly, comparative genomics, and haplotype segregation
Phase Genomics
Using Proximity to Fix Assembly
Genome Assessment
BUSCO
Additional QA/QC and metrics
ETC
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

Closing Thoughts

Prerequisites for bioinformatics

The bottom line

Next Steps

My recommendation is to follow all of the instructions again, from the beginning on your own and send emails to training.bioinformatics@ucdavis.edu And we will be responsive to answering questions

Upcoming Workshops

Now in our 13th year of training researchers, the UC Davis Bioinformatics Core invites you to attend one or more of our 2020 workshops. The following workshops are suitable for beginners to advanced researchers, and are also of interest to those with some data analysis experience.

Jul 27 - Jul 31, 2020 RNA-Seq Workshop @ UC Davis
Aug 12 - Aug 14, 2020 Introduction to Single Cell RNA-Seq @ UC Davis
Aug 17 - Aug 19, 2020 Advanced Single Cell RNA-Seq @ UC Davis
Oct 5 - Oct 9, 2020 Bioinformatics: Command Line/R Prerequisites
Nov 30 - Dec 4, 2020 Introduction to Analysis of Epigenetic Data

For more information on these and other events, and to register, go to https://registration.genomecenter.ucdavis.edu/

Previous Workshops available online

If you would like to take a look at the documentation from previous workshops.

Questions?

Contact us at training.bioinformatics@ucdavis.edu

If you receive email directly from training.bioinformatics@ucdavis.edu, you are currently subscribed to one of our announcements lists. To subscribe / unsubscribe from the Bioinformatics Core email lists, please follow the instructions at the bottom of http://bioinformatics.ucdavis.edu/contact-us/.