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teaching:2025winter:algbioinf [2025/10/22 09:12]
luca 		teaching:2025winter:algbioinf [2025/12/10 14:21] (current)
luca [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 ====
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 | 19.11. | Pseudocode presentation | | 19.11. | Pseudocode presentation |
 | 26.11. | k-mer counting challenge | Everybody |  | 26.11. | k-mer counting challenge | Everybody | 
-| 3.12. | -- | +| 3.12. | Mitan | Sparse and skew hashing of K-mers. | 
-| 10.12. | -- | +| 10.12. | Kiril | Space-efficient and exact de Bruijn graph representation based on a Bloom filter. (Minia)| 
-| 17.12. | -- | +| 17.12. | -- |   
-| 14.1. | -- | +| 14.1. | Tom | Velvet: algorithms for de novo short read assembly using de Bruijn graphs. ​| 
-| 21.1. | -- | +| 21.1. | Nils & John |Mash: fast genome and metagenome distance estimation using MinHash. ​ &   Fast gapped k-mer (cuckoo hash tables)  ​|  
-| 28.1. | -- | +| 28.1. | Mehran | Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time. |  
-| 4.2. | -- | +| 4.2. | Nicola ​| Efficient q-gram filters ​| 
-| 11.2. | -- | +| 25.2. | Elif | Fimpera ​| 
-| 25.2. | -- |+
 | 4.3. | -- | | 4.3. | -- |
 | 11.3. | -- | | 11.3. | -- |
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   * Multiple fasta file, containing nucleotide sequences (small or capital letters, maybe N's)   * Multiple fasta file, containing nucleotide sequences (small or capital letters, maybe N's)
   * //k//-mer length **k**   * //k//-mer length **k**
-  * threshold ​**c**+  * cutoff ​**c** : a //k//-mer must appear at least **c** times in the same fasta file to be counted.
  
 **Output:** **Output:**