Table of Contents

Notes

Spring 2015

For syllabus and note taker schedule please see the spring_2015_syllabus

Date Topic
Mon Mar 30 09:30-10:40 Course outline
Wed Apr 1 09:30-10:40 Banana slug biology
Fri Apr 3 09:30-10:40 Dissection, extraction, and library preparation
Mon Apr 6 09:30-10:40 Denovo-assembly part:1
Wed Apr 8 09:30-10:40 Denovo-assembly part:2
Fri Apr 10 09:30-10:40 Denovo-assembly part:3
Mon Apr 13 09:30-10:40 Illumina sequencing technology
Wed Apr 15 09:30-10:40 K-mer spectra analysis
Fri Apr 17 09:30-10:40 Genome assembly - theory and practice
Mon Apr 20 09:30-10:40 Team 1 report
Wed Apr 22 09:30-10:40 Team 2 report
Fri Apr 24 09:30-10:40 Team 3 report
Mon Apr 27 09:30-10:40 Team 4 report
Wed Apr 29 09:30-10:40 Team 5 report
Fri May 1 09:30-10:40 Population genetics
Mon May 4 09:30-10:40 Mate pair libraries
Wed May 6 09:30-10:40 RNAseq
Fri May 8 09:30-10:40 Strategy Session
Mon May 11 09:30-10:40 Team 1 report
Wed May 13 09:30-10:40 Team 2 report
Fri May 15 09:30-10:40 Team 3 report
Mon May 18 09:30-10:40 Team 4 report
Wed May 20 09:30-10:40 Team 5 report
Fri May 22 09:30-10:40 Assembly of repeat regions
Mon May 25 09:30-10:40 Holiday
Wed May 27 09:30-10:40 Genome annotation
Fri May 29 09:30-10:40 Jellyfish internals for kmer counting
Mon Jun 1 09:30-10:40 Burrows-Wheeler transform
Wed Jun 3 09:30-10:40 Lecture title
Fri Jun 5 09:30-10:40 Final analysis II

Spring 2011

Date Topic
Mon Mar 28 14:00-15:10 Course Outline
Wed Mar 30 14:00-15:10 Sequencing Technologies
Fri Apr 1 14:00-15:10 Guest Lecture: Nader Pourmand on Sequencing Technologies
Mon Apr 4 14:00-15:10 Assembly Overview
Wed Apr 6 14:00-15:10 Jellyfish
Fri Apr 8 14:00-15:10 Jellyfish Results
Mon Apr 11 14:00-15:10 Guest Lecture: Graham Ruby on PRICE
Wed Apr 13 14:00-15:10 Guest Lecture: Daniel Zerbino on Velvet
Fri Apr 15 14:00-15:00 Resources
Mon Apr 18 14:00-15:00 Game Plan
Wed Apr 20 14:00-15:00 More Jellyfish
Fri Apr 22 14:00-15:00 Burrows-Wheeler Transform
Mon Apr 25 14:00-15:00 More Burrows-Wheeler Transform
Wed Apr 27 14:00-15:00 454 Presentation
Fri Apr 29 14:00-15:00 Guest Lecture: Janet Leonard and John Pearse on Banana Slug Biology
Mon May 9 14:00-15:00 Quake paper: Edward Liaw
Wed May 11 14:00-15:00 SOAP-denovo paper: Sam Vohr
Fri May 13 14:00-15:00 BWA results, insert length analysis
Mon May 16 14:00-15:00 Seqprep
Wed May 18 14:00-15:00 K-mer Counting Theory
Fri May 20 14:00-15:00 Sanger String Graph Assembler
Mon May 23 14:00-15:00 Guest Lecture: Patricia Chan on setting up the UCSC Genome Browser
Wed May 25 14:00-15:00 Paired End Assembler
Fri May 27 14:00-15:00 Review
Fri June 3 14:00-15:00 SARUMAN Paper: Sam Vohr

Spring 2010

Date Topic
Mon Mar 29 14:00-15:10 Course Outline
Wed Mar 31 14:00-15:10 Sequencing Technologies
Fri Apr 02 14:00-15:10 Resources
Mon Apr 05 14:00-15:10 Assembly Overview
Wed Apr 07 14:00-15:10 Base Space, Flow Space, Color Space
Fri Apr 09 14:00-15:10 Assembler Graphs
Mon Apr 12 14:00-15:10 Sample Preparation
Wed Apr 14 14:00-15:10 Library Construction
Fri Apr 16 14:00-15:10 Newbler Assembly on POG
Mon Apr 19 14:00-15:10 Presentation on Assemblers and Velvet
Wed Apr 21 14:00-15:10 Newbler Assembly on POG and using Solid Mate Pair Data
Fri Apr 23 14:00-15:10 Banana Slug Biology - Guest Lecture
Mon Apr 26 14:00-15:10 Tool Review: Galt and Velvet
Wed Apr 28 14:00-15:10 Tool Review: Euler-SR (John) and MIRA (Michael)
Fri Apr 30 14:00-15:10 map-colorspace5 and contig ordering; Estimating Genome Size
Mon May 03 14:00-15:10 Burrows Wheeler Transform
Wed May 05 14:00-15:10 Mate-paired data to fix assembly
Fri May 07 14:00-15:10 Approximate Search and BWA
Mon May 10 14:00-15:10 Tool Review : SSAKE by John Kim, and Slug locomotion by Jenny
Wed May 12 14:00-15:10 Tool Review : PCAP by Shyamini
Fri May 14 14:00-15:10 No class
Mon May 17 14:00-15:10 Genome Annotation with RAST and Artemis by Jeff Long
Wed May 19 14:00-15:10 Thomas Juetteman on ALLPATHS, Michael on Mira Internals
Fri May 21 14:00-15:10 Patricia Chan on setting up a genome browser
Mon May 24 14:00-15:10 Slug assemblies and pluck-scripts
Wed May 26 14:00-15:10 pluck-scripts
Fri May 28 14:00-15:10 pluck-scripts cont.
Wed Jun 02 14:00-15:10 Looking at related de-novo assemblies: Sea Hare and Panda
Fri Jun 04 14:00-15:10 Pcap Pog Assembly and Colorspace Python Script