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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

Logging In & Transferring Files

You should already have an account on our systems

For Macs/Linux - Logging In

  1. Open a Terminal (usually under Applications/Utilities on a Mac), or install iterm2
  2. Cut and paste this into the terminal:

    ssh username@tadpole.genomecenter.ucdavis.edu

where ‘username’ is replaced with your username. Press Enter.

  1. Type in your password. No characters will display when you are typing. Press Enter.

For Macs/Linux - Transferring files

  1. Use scp (secure copy, a remote file copying program):

    scp username@tadpole.genomecenter.ucdavis.edu:full/path/to/file .

  2. Replace ‘username’ with your username and replace ‘full/path/to/file’ with the full path to the file you want to transfer. Note that there is a “.” at the end of the command, which is where to put the file, i.e. your current directory. You will have to type in your password.

For Windows - Logging In

Windows needs a terminal to connect with, you have a few options:

  1. Shell for Windows 10
  2. Enable SSH OR
  3. MobaXterm
  4. PuTTY

In putty, mobaxterm:

  1. Open up terminal.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Make sure the Connection Type is SSH.
  4. Press “Open”. It will ask you for your username and password.

In Shell with SSH enabled:

ssh username@tadpole.genomecenter.ucdavis.edu

where ‘username’ is replaced with your username. Press Enter.

For Windows - Transferring files

  1. Open up WinSCP. If you haven’t installed it, get WinSCP here.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Type in your username and password.
  4. Make sure the File Protocol is SFTP.
  5. Press “Login”.