Workshop Materials
Workshop Materials
Embedded Files
Wetlab Lab Notebook
Wetlab Lab Notebook
Click on the button below to access the protocols that we used in the wetlab portion of the workshop. We used the QIAGEN Genomic Tip kit because it usually yields the cleanest and longest DNA, but there are many other HMW DNA kits available and may be better for different needs and sample types.
Click on the buttons below to download the "reads" used for the exercise and the answer.
Hands-on genome assembly exercise
Hands-on genome assembly exercise
Directions for the exercise start on slide 17 of Day 1 slides, but I highly encourage you to look at all of the material prior. The goal of this exercise is to understand how coverage, read length, and error rate affect genome assembly.
Phase 1: Short-read assembly
Consider the amount of overlap of the reads and evenness of coverage
Simulation of 4bp reads, no errors
Read orientation: triangles should be pointing up, black square positioned slightly to the left
Linear genome
Phase 2: Hybrid assembly
Consider the amount of overlap of the reads and evenness of coverage
Simulation of 4bp reads + long reads
Blacked out squares in long reads are “errors” and can be any base
Lecture Slides
Lecture Slides
We tried to record the lectures, but unfortunately we had technical issues and couldn't record most of them.
Note that Day 3 has some repeat information from Days 1 and 2 because it was hybrid.
If you would like to have PDFs of the slides or use the material please email Lauren (lmlui at lbl dot gov)
AndrewWilson.mp4Leveraging Long Reads for Synthetic Biology
Leveraging Long Reads for Synthetic Biology
Andrew Wilson, Pacific Northwest NationalLaboratory
day3.mp4Day 3 Introduction
Day 3 Introduction
Lauren Lui, Lawrence Berkeley National Laboratory
Nanopore Basecalling
Nanopore Basecalling
Torben Nielsen, Lawrence Berkeley National Laboratory
day3-basecalling-edit.mp4day3-narrative.mp4The bug we found in Flye during the workshop has now been fixed.
Example KBase Narrative for Long Read Assembly
Example KBase Narrative for Long Read Assembly
John-Marc Chandonia and Lauren Lui, Lawrence Berkeley National Laboratory
KBase Pipelines
KBase Pipelines
Ben Allen, Oak Ridge National Laboratory, KBase
BenAllen.mp4Elisha.mp4Publishing with KBase
Publishing with KBase
Elisha Wood-Charlson, Lawrence Berkeley National Laboratory, KBase
Polishing a Genome: de novo assembly of bacterial genomes in a 200-level class
Polishing a Genome: de novo assembly of bacterial genomes in a 200-level class
Carlos Goller, North Carolina State University
Carlos.mp4LaurenLui.mp4Pushing the Limits of Long Read Metagenomics
Pushing the Limits of Long Read Metagenomics
Lauren Lui, Lawrence Berkeley National Laboratory
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