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teaching:2025winter:algbioinf [2025/10/22 11:14]
luca 		teaching:2025winter:algbioinf [2025/12/10 14:21] (current)
luca [Timetable]
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 | 3.12. | Mitan | Sparse and skew hashing of K-mers. | | 3.12. | Mitan | Sparse and skew hashing of K-mers. |
 | 10.12. | Kiril | Space-efficient and exact de Bruijn graph representation based on a Bloom filter. (Minia)| | 10.12. | Kiril | Space-efficient and exact de Bruijn graph representation based on a Bloom filter. (Minia)|
-| 17.12. | Nicola | Efficient q-gram filters ​| +| 17.12. | -- |   
-| 14.1. | Tom | Tom Velvet: algorithms for de novo short read assembly using de Bruijn graphs. | +| 14.1. | Tom | Velvet: algorithms for de novo short read assembly using de Bruijn graphs. | 
-| 21.1. | Nils |Mash: fast genome and metagenome distance estimation using MinHash. |  +| 21.1. | Nils & John |Mash: fast genome and metagenome distance estimation using MinHash. ​ & ​  Fast gapped k-mer (cuckoo hash tables)  ​|  
-| 28.1. | Tom |Velvet: algorithms for de novo short read assembly using de Bruijn graphs. |  +| 28.1. | Mehran | Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time. |  
-| 4.2. | Mehran | Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time. |  +| 4.2. | Nicola ​| Efficient q-gram filters ​| 
-| 11.2. | John | Bifrost ​| +| 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:**