Banana Slug Genomics

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=== Spring 2015 Syllabus ===
Class meets M/W/F 9:30-10:40 in PSB 305

For a list of past/present lecture notes please see the [[lecture notes]]

| Number | Date | Topic | Lecturer | Lecture Notes | Note taker 1 | Note taker 2 | Slides |
| 1  | 30 Mar | Course overview & introduction | Green/Karplus | [[lecture_notes:03-30-2015]] | Dudek | Eisenhart |
| 2  | 1 Apr | The biology of the banana slug | Leonard / Pearse | [[lecture_notes:04-01-2015]] | Matthew | Saremi |
| 3  | 3 Apr | Disection and sequencing libraries | Weber / Green | [[lecture_notes:04-03-2015]] | Richardson | Hussain | {{lecture_notes:slug_presentation.pdf|Banana slug genome project}} |
| 4  | 6 Apr | De novo genome assembly I   | Prost | [[lecture_notes:04-06-2015]] | Kan | Chaves | {{::genomics_workshop_ucsc.pdf|}} |
| 5  | 8 Apr | De novo genome assembly II  | Prost | [[lecture_notes:04-08-2015]] | Hussain |jolespin | {{::genomics_workshop_ucsc.pdf|}} |
| 6  | 10 Apr | De novo genome assembly III | Prost | [[lecture_notes:04-10-2015]] | Musselman-Brown |jolespin | {{::genomics_workshop_ucsc.pdf|}} |
| 7  | 13 Apr | Illumina sequencing technology | Green | [[lecture_notes:04-13-2015]] | Hussain  |Eisenhart | {{:illumina-sequencing-v1.pdf|Illumina slides}} |
| 8  | 15 Apr | k-mer spectra analysis | Green | [[lecture_notes:04-15-2015]] | Musselman-Brown | Cole | {{::k-mers-v1.pdf| k-mer slides}}|
| 9  | 17 Apr | Genome assembly - theory and practice | Green | [[lecture_notes:04-17-2015]] | Hussain |Cole | {{:dbg-assembly-v1.pdf| DBG-assembly slides}}|
| 10  | 20 Apr | Team 1 report | Team 1 | [[lecture_notes:04-20-2015]] | Chaves| Calef |{{bme_235_meraculous_report_1.pdf|Meraculous: Team 1 Report}}|
| 11  | 22 Apr | Team 2 report | Team 2 | [[lecture_notes:04-22-2015]] | McGovern | Cole | {{:lecture_notes:soap_team2_report.pdf| SOAPdenovo: Team 2 Report}}|
| 12  | 24 Apr | Team 3 report | Team 3 | [[lecture_notes:04-24-2015]] | Richardson | Houser | {{:sga_bme235_s15.pdf| SGA: Team 3 Report}}|
| 13  | 27 Apr | Team 4 report | Team 4 | [[lecture_notes:04-26-2015]] | Houser |Chaves| {{:abysspresentation1.pdf| ABySS: Team 4 Report}} |
| 14  | 29 Apr | Team 5 report | Team 5 | [[lecture_notes:04-29-2015]] | Richardson | Kan |{{:team_5_report_1.pdf| Discovar de novo: Team 5 Report}} |
| 15  | 1 May | Population genetics / [[http://www.nature.com/nature/journal/v475/n7357/full/nature10231.html|PSMC]] | Green | [[lecture_notes:05-01-2015]] | Saremi | Markello |
| 16  | 4 May | Mate-pair libraries | Weber/O'Connell | [[lecture_notes:05-04-2015]] | Musselman-Brown | Cole |{{:slug_mate_pair_presentation.pdf|Mate Pair Libraries}}|
| 17  | 6 May | RNAseq | Katzman | [[lecture_notes:05-06-2015]] | Dudek | Chaves |{{:rnaseq.pdf|RNA-seq}}; {{:trapnell_et_al._2010.pdf|Trapnell et al., 2010}}|
| 18  | 8 May | Strategy session | Karplus/class | [[lecture_notes:05-08-2015]] | Saremi | Markello |
| 19  | 11 May | Team 1 report | Team 1 | [[lecture_notes:05-11-2015]] | Eisenhart | Matthew |{{:bme235_meraculous_report_2.pdf|}}|
| 20  | 13 May | Team 2 report | Team 2 | [[lecture_notes:05-13-2015]] |Feal | Calef | {{:soapassembly2_update.pptx.pdf| Team 2 SOAPdenovo2 update}}|
| 21  | 15 May | Team 3 report | Team 3 | [[lecture_notes:05-15-2015]] | Chaves| Calef |
| 22  | 18 May | Team 4 report | Team 4 | [[lecture_notes:05-18-2015]] | Musselman-Brown | McGovern|
| 23  | 20 May | Team 5 report | Team 5 | [[lecture_notes:05-20-2015]] | jolespin | Saremi |{{:discovar_team_presentation_2.pdf|}} |
| 24  | 22 May | Assembly of Repeat regions |  | [[lecture_notes:05-22-2015]] | JaredC | Saremi |
| -  | 25 May | Holiday | N/A | N/A | N/A | N/A |
| 25  | 27 May | Genome Annotation {{lecture_notes:eukgeneannotation.pdf|Annotation Review paper}} | Prost | [[lecture_notes:05-27-2015]] | Kan| Feal| {{::annotation_workshop_ucsc.pdf}}|
| 26  | 29 May |Jellyfish internals for kmer counting  | Karplus | [[lecture_notes:05-29-2015]] | Kan| JaredC |
| 27  | 1 Jun | Burrows-Wheeler transform (guts of most mappers) | Karplus | [[lecture_notes:06-01-2015]] | JaredC | Markello |
| 28  | 3 Jun |  |  | [[lecture_notes:06-03-2015]] |Feal | Calef|
| 29  | 5 Jun | Final analysis II | Green | [[lecture_notes:06-05-2015]] | JaredC | Dudek |
Banana Slug Genomics

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