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archive:spring_2015_syllabus [2015/04/17 18:03] ed |
archive:spring_2015_syllabus [2015/04/18 21:05] charles |
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| 1 | 30 Mar | Course overview & introduction | Green/Karplus | [[lecture_notes:03-30-2015]] | Dudek | Eisenhart | | | 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 | | | 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 | | + | | 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 | | | 4 | 6 Apr | De novo genome assembly I | Prost | [[lecture_notes:04-06-2015]] | Kan | Chaves | | ||
| 5 | 8 Apr | De novo genome assemlby II | Prost | [[lecture_notes:04-08-2015]] | Hussain |jolespin | | | 5 | 8 Apr | De novo genome assemlby II | Prost | [[lecture_notes:04-08-2015]] | Hussain |jolespin | | ||
| 6 | 10 Apr | De novo genome assembly III | Prost | [[lecture_notes:04-10-2015]] | Musselman-Brown |jolespin | | | 6 | 10 Apr | De novo genome assembly III | Prost | [[lecture_notes:04-10-2015]] | Musselman-Brown |jolespin | | ||
- | | 7 | 13 Apr | Illumina sequencing technology | Green | [[lecture_notes:04-13-2015]] | Hussain |Eisenhart | [[Illumina-tech-slides|lecture_notes:illumina-sequencing-v1.ppt]] | | + | | 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-mer-slides | | | 8 | 15 Apr | k-mer spectra analysis | Green | [[lecture_notes:04-15-2015]] | Musselman-Brown | Cole | k-mer-slides | | ||
| 9 | 17 Apr | Genome assembly - theory and practice | Green | [[lecture_notes:04-17-2015]] | Hussain |Cole | DBG-assembly-slides | | | 9 | 17 Apr | Genome assembly - theory and practice | Green | [[lecture_notes:04-17-2015]] | Hussain |Cole | DBG-assembly-slides | | ||
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| 25 | 27 May | | | [[lecture_notes:05-27-2015]] | Kan| | | | 25 | 27 May | | | [[lecture_notes:05-27-2015]] | Kan| | | ||
| 26 | 29 May |Jellyfish internals for kmer counting | Karplus | [[lecture_notes:05-29-2015]] | Kan| JaredC | | | 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 | | | + | | 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]] | | | | | 28 | 3 Jun | | | [[lecture_notes:06-03-2015]] | | | | ||
| 29 | 5 Jun | Final analysis II | Green | [[lecture_notes:06-05-2015]] | JaredC | | | | 29 | 5 Jun | Final analysis II | Green | [[lecture_notes:06-05-2015]] | JaredC | | |