Banana Slug Genomics

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====== Notes ======

===== Spring 2015 =====
For syllabus and note taker schedule please see the [[archive:spring_2015_syllabus]]

^ Date ^ Topic ^
| Mon Mar  30 09:30-10:40 | [[lecture_notes:03-30-2015|Course outline]] |
| Wed Apr  1  09:30-10:40 | [[lecture_notes:04-01-2015|Banana slug biology]] |
| Fri Apr  3  09:30-10:40 | [[lecture_notes:04-03-2015|Dissection, extraction, and library preparation]] |
| Mon Apr  6  09:30-10:40 | [[lecture_notes:04-06-2015|Denovo-assembly part:1]] |
| Wed Apr  8  09:30-10:40 | [[lecture_notes:04-08-2015|Denovo-assembly part:2]] |
| Fri Apr  10 09:30-10:40 | [[lecture_notes:04-10-2015|Denovo-assembly part:3]] |
| Mon Apr  13 09:30-10:40 | [[lecture_notes:04-13-2015|Illumina sequencing technology]] |
| Wed Apr  15 09:30-10:40 | [[lecture_notes:04-15-2015|K-mer spectra analysis]] |
| Fri Apr  17 09:30-10:40 | [[lecture_notes:04-17-2015|Genome assembly - theory and practice]] | 
| Mon Apr  20 09:30-10:40 | [[lecture_notes:04-20-2015|Team 1 report]] |
| Wed Apr  22 09:30-10:40 | [[lecture_notes:04-22-2015|Team 2 report]] |
| Fri Apr  24 09:30-10:40 | [[lecture_notes:04-24-2015|Team 3 report]] |
| Mon Apr  27 09:30-10:40 | [[lecture_notes:04-27-2015|Team 4 report]] |
| Wed Apr  29 09:30-10:40 | [[lecture_notes:04-29-2015|Team 5 report]] |
| Fri May  1  09:30-10:40 | [[lecture_notes:05-01-2015|Population genetics]] |
| Mon May  4  09:30-10:40 | [[lecture_notes:05-04-2015|Mate pair libraries]] |
| Wed May  6  09:30-10:40 | [[lecture_notes:05-06-2015|RNAseq]] |
| Fri May  8  09:30-10:40 | [[lecture_notes:05-08-2015|Strategy Session]] |
| Mon May  11 09:30-10:40 | [[lecture_notes:05-11-2015|Team 1 report]] |
| Wed May  13 09:30-10:40 | [[lecture_notes:05-13-2015|Team 2 report]] |
| Fri May  15 09:30-10:40 | [[lecture_notes:05-15-2015|Team 3 report]] |
| Mon May  18 09:30-10:40 | [[lecture_notes:05-18-2015|Team 4 report]] |
| Wed May  20 09:30-10:40 | [[lecture_notes:05-20-2015|Team 5 report]] |
| Fri May  22 09:30-10:40 | [[lecture_notes:05-22-2015|Assembly of repeat regions]] |
| Mon May  25 09:30-10:40 | Holiday |
| Wed May  27 09:30-10:40 | [[lecture_notes:05-27-2015|Genome annotation]] |
| Fri May  29 09:30-10:40 | [[lecture_notes:05-29-2015|Jellyfish internals for kmer counting]] |
| Mon Jun  1  09:30-10:40 | [[lecture_notes:06-01-2015|Burrows-Wheeler transform]] |
| Wed Jun  3  09:30-10:40 | [[lecture_notes:06-03-2015|Lecture title]] |
| Fri Jun  5  09:30-10:40 | [[lecture_notes:06-05-2015|Final analysis II]] |

===== Spring 2011 =====

^ Date ^ Topic ^
| Mon Mar 28 14:00-15:10 | [[lecture_notes:03-28-2011|Course Outline]] |
| Wed Mar 30 14:00-15:10 | [[lecture_notes:03-30-2011|Sequencing Technologies]] |
| Fri Apr  1 14:00-15:10 | [[lecture_notes:04-01-2011|Guest Lecture: Nader Pourmand on Sequencing Technologies]] |
| Mon Apr  4 14:00-15:10 | [[lecture_notes:04-04-2011|Assembly Overview]] |
| Wed Apr  6 14:00-15:10 | [[lecture_notes:04-07-2011|Jellyfish]] |
| Fri Apr  8 14:00-15:10 | [[lecture_notes:04-08-2011|Jellyfish Results]] |
| Mon Apr 11 14:00-15:10 | [[lecture_notes:04-11-2011|Guest Lecture: Graham Ruby on PRICE]] |
| Wed Apr 13 14:00-15:10 | [[lecture_notes:04-13-2011|Guest Lecture: Daniel Zerbino on Velvet]] |
| Fri Apr 15 14:00-15:00 | [[lecture_notes:04-15-2011|Resources]] |
| Mon Apr 18 14:00-15:00 | [[lecture_notes:04-18-2011|Game Plan]] |
| Wed Apr 20 14:00-15:00 | [[lecture_notes:04-20-2011|More Jellyfish]] |
| Fri Apr 22 14:00-15:00 | [[lecture_notes:04-22-2011|Burrows-Wheeler Transform]] |
| Mon Apr 25 14:00-15:00 | [[lecture_notes:04-25-2011|More Burrows-Wheeler Transform]] |
| Wed Apr 27 14:00-15:00 | [[lecture_notes:04-27-2011|454 Presentation]] |
| Fri Apr 29 14:00-15:00 | [[lecture_notes:04-29-2011|Guest Lecture: Janet Leonard and John Pearse on Banana Slug Biology]] |
| Mon May  9 14:00-15:00 | [[lecture_notes:05-09-2011|Quake paper: Edward Liaw]] |
| Wed May 11 14:00-15:00 | [[lecture_notes:05-11-2011|SOAP-denovo paper: Sam Vohr]] |
| Fri May 13 14:00-15:00 | [[lecture_notes:05-13-2011|BWA results, insert length analysis]] |
| Mon May 16 14:00-15:00 | [[lecture_notes:05-16-2011|Seqprep]] |
| Wed May 18 14:00-15:00 | [[lecture_notes:05-18-2011|K-mer Counting Theory]] |
| Fri May 20 14:00-15:00 | [[lecture_notes:05-20-2011|Sanger String Graph Assembler]] |
| Mon May 23 14:00-15:00 | [[lecture_notes:05-23-2011|Guest Lecture: Patricia Chan on setting up the UCSC Genome Browser]] |
| Wed May 25 14:00-15:00 | [[lecture_notes:05-25-2011|Paired End Assembler]] |
| Fri May 27 14:00-15:00 | [[lecture_notes:05-27-2011|Review]] |
| Fri June 3 14:00-15:00 | [[lecture_notes:06-03-2011|SARUMAN Paper: Sam Vohr]] |
===== Spring 2010 =====
^ Date ^ Topic ^
| Mon Mar 29 14:00-15:10 | [[lecture_notes:03-29-2010|Course Outline]] |
| Wed Mar 31 14:00-15:10 | [[lecture_notes:03-31-2010|Sequencing Technologies]] |
| Fri Apr 02 14:00-15:10 | [[lecture_notes:04-02-2010|Resources]] |
| Mon Apr 05 14:00-15:10 | [[lecture_notes:04-05-2010|Assembly Overview]] |
| Wed Apr 07 14:00-15:10 | [[lecture_notes:04-07-2010|Base Space, Flow Space, Color Space]] |
| Fri Apr 09 14:00-15:10 | [[lecture_notes:04-09-2010|Assembler Graphs]] |
| Mon Apr 12 14:00-15:10 | [[lecture_notes:04-12-2010|Sample Preparation]] |
| Wed Apr 14 14:00-15:10 | [[lecture_notes:04-14-2010|Library Construction]] |
| Fri Apr 16 14:00-15:10 | [[lecture_notes:04-16-2010|Newbler Assembly on POG]] |
| Mon Apr 19 14:00-15:10 | [[lecture_notes:04-19-2010|Presentation on Assemblers and Velvet]] |
| Wed Apr 21 14:00-15:10 | [[lecture_notes:04-21-2010|Newbler Assembly on POG and using Solid Mate Pair Data]] |
| Fri Apr 23 14:00-15:10 | [[lecture_notes:04-23-2010|Banana Slug Biology - Guest Lecture]] |
| Mon Apr 26 14:00-15:10 | [[lecture_notes:04-26-2010|Tool Review: Galt and Velvet]] |
| Wed Apr 28 14:00-15:10 | [[lecture_notes:04-28-2010|Tool Review: Euler-SR (John) and MIRA (Michael)]] |
| Fri Apr 30 14:00-15:10 | [[lecture_notes:04-30-2010|map-colorspace5 and contig ordering; Estimating Genome Size]] |
| Mon May 03 14:00-15:10 | [[lecture_notes:05-03-2010|Burrows Wheeler Transform]] |
| Wed May 05 14:00-15:10 | [[lecture_notes:05-05-2010|Mate-paired data to fix assembly]] |
| Fri May 07 14:00-15:10 | [[lecture_notes:05-07-2010|Approximate Search and BWA]] |
| Mon May 10 14:00-15:10 | [[lecture_notes:05-10-2010|Tool Review : SSAKE by John Kim, and Slug locomotion by Jenny]] |
| Wed May 12 14:00-15:10 | [[lecture_notes:05-12-2010|Tool Review : PCAP by Shyamini]] |
| Fri May 14 14:00-15:10 | No class |
| Mon May 17 14:00-15:10 | [[lecture_notes:05-17-2010|Genome Annotation with RAST and Artemis by Jeff Long]]|
| Wed May 19 14:00-15:10 | [[lecture_notes:05-19-2010|Thomas Juetteman on ALLPATHS, Michael on Mira Internals]]|
| Fri May 21 14:00-15:10 | [[lecture_notes:05-21-2010|Patricia Chan on setting up a genome browser]]|
| Mon May 24 14:00-15:10 | [[lecture_notes:05-24-2010|Slug assemblies and pluck-scripts]]|
| Wed May 26 14:00-15:10 | [[lecture_notes:05-26-2010|pluck-scripts]]|
| Fri May 28 14:00-15:10 | [[lecture_notes:05-28-2010|pluck-scripts cont.]]|
| Wed Jun 02 14:00-15:10 | [[lecture_notes:06-02-2010|Looking at related de-novo assemblies: Sea Hare and Panda]]|
| Fri Jun 04 14:00-15:10 | [[lecture_notes:06-04-2010|Pcap Pog Assembly and Colorspace Python Script]]|
Banana Slug Genomics

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