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teaching:2025summer:kmer_algbioinf [2025/04/09 10:07]
rwittler 		teaching:2025summer:kmer_algbioinf [2025/06/17 09:05] (current)
rwittler [Timetable]
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   * Giulio Ermanno Pibir. "​Sparse and skew hashing of K-mers."​ [[https://​academic.oup.com/​bioinformatics/​article/​38/​Supplement_1/​i185/​6617506?​login=true|Bioinformatics 38.Suppl1 (2022):​i185-i194.]]   * Giulio Ermanno Pibir. "​Sparse and skew hashing of K-mers."​ [[https://​academic.oup.com/​bioinformatics/​article/​38/​Supplement_1/​i185/​6617506?​login=true|Bioinformatics 38.Suppl1 (2022):​i185-i194.]]
  
 +==== Pangenomics ====
  
 +  * Luca Parmigiani, Roland Wittler, and Jens Stoye. “Revisiting pangenome openness with k-mers.” [[https://​peercommunityjournal.org/​item/​10.24072/​pcjournal.415.pdf|Peer Community Journal (4):e47 (2024)]] ​
  
 ==== Timetable ==== ==== Timetable ====
  
 | 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. |  | +| 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. |  |+| 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. |  | +| 07.05. | Pseudocode vorstellen ​| 
-| 14.05. |  | +| 14.05. | KMC 3: counting and manipulating //k//-mer statistics | Kathrin ​| 
-| 21.05. |  |+| 21.05. | k-mer counting challenge | (fast) alle | 
 | 28.05. | -- | | 28.05. | -- |
-| 04.05. |  | +| 04.06. | Fast gapped //k//-mer counting with subdivided multi-way bucketed Cuckoo hash table | Sofie  | 
-| 11.06. |  | +|            | Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer | Liliana ​| 
-| 18.06. |  | +| 11.06. | Sparse and skew hashing of K-mers | Alena | 
-| 25.06. |  |+| 18.06. | Space-efficient and exact de Bruijn graph representation based on a Bloom filter. (Minia) | Max | 
 +| 25.06. | Minimap2: pairwise alignment for nucleotide sequences | Igor | 
 +|             | Revisiting pangenome openness with k-mers | Mathis ​|
 | 02.07. | -- | | 02.07. | -- |
-| 09.07. |  |+| 09.07. | |
 | 16.07. | -- | | 16.07. | -- |