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teaching:2025summer:kmer_algbioinf [2025/04/16 09:47]
rwittler 		teaching:2025summer:kmer_algbioinf [2025/06/17 09:05] (current)
rwittler [Timetable]
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 | 09.04. | Organization, ​ topic selection, Scientific reading ​ | {{:​teaching:​2022summer:​algbioinf:​howtoread.pdf|Slides:​ HowToRead}} | | 09.04. | Organization, ​ topic selection, Scientific reading ​ | {{:​teaching:​2022summer:​algbioinf:​howtoread.pdf|Slides:​ HowToRead}} |
-| 16.04. | Pseudocode | [[https://​texdoc.org/​serve/​algorithm2e/​0|algorithm2e-docu]],​ {{:​teaching:​2025summer:​kmer:​template_algo.tex.pdf|LaTeX template (remove .pdf from file name)}} | +| 16.04. | Pseudocode | [[https://​texdoc.org/​serve/​algorithm2e/​0|algorithm2e-docu]],​ {{:​teaching:​2025summer:​kmer:​template_algo.tex.pdf|LaTeX template (remove .pdf from file name)}}, {{:​teaching:​2025summer:​kmer:​template_algo.pdf|notes/​example}} | 
-| 23.04. | Wissenschaftliches Schreiben und Präsentieren ​|+| 23.04. | -- (self study) | [[:​teaching:​2024summer:​karp:​writing|Scientific Writing]], [[https://​doi.org/​10.1371/​journal.pcbi.0030077|Ten Simple Rules for Making Good Oral Presentations,​ Philip E Bourne]], [[https://​doi.org/​10.1371/​journal.pcbi.1005373|Ten simple rules for short and swift presentations,​ Christopher J. Lortie]] ​|
 | 30.04. | -- | | 30.04. | -- |
 | 07.05. | Pseudocode vorstellen | | 07.05. | Pseudocode vorstellen |
 | 14.05. | KMC 3: counting and manipulating //k//-mer statistics | Kathrin | | 14.05. | KMC 3: counting and manipulating //k//-mer statistics | Kathrin |
-|            | Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer | Liliana | 
 | 21.05. | k-mer counting challenge | (fast) alle |  | 21.05. | k-mer counting challenge | (fast) alle | 
 | 28.05. | -- | | 28.05. | -- |
-| 04.05. | Fast gapped //k//-mer counting with subdivided multi-way bucketed Cuckoo hash table | Sofie  | +| 04.06. | Fast gapped //k//-mer counting with subdivided multi-way bucketed Cuckoo hash table | Sofie  ​| 
-| 11.06. | Velvet: algorithms for de novo short read assembly using de Bruijn graphs ​| Simon |+|            | Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer | Liliana ​| 
 +| 11.06. | Sparse and skew hashing of K-mers ​| Alena |
 | 18.06. | Space-efficient and exact de Bruijn graph representation based on a Bloom filter. (Minia) | Max | | 18.06. | Space-efficient and exact de Bruijn graph representation based on a Bloom filter. (Minia) | Max |
-|            | Minimap2: pairwise alignment for nucleotide sequences | Igor | +| 25.06. ​| Minimap2: pairwise alignment for nucleotide sequences | Igor | 
-| 25.06. ​| Revisiting pangenome openness with k-mers | Mathis |+|             ​| Revisiting pangenome openness with k-mers | Mathis |
 | 02.07. | -- | | 02.07. | -- |
 | 09.07. | | | 09.07. | |