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--- teaching:2025winter:algbioinf [2025/10/22 09:44]
luca [Pangenomics]
+++ teaching:2025winter:algbioinf [2025/12/10 14:21] (current)
luca [Timetable]
@@ Line 57: / Line 57: @@
 | 19.11. | Pseudocode presentation |
 | 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. | -- |
-| 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. | -- |
 | 11.3. | -- |
@@ Line 76: / Line 75: @@
   * Multiple fasta file, containing nucleotide sequences (small or capital letters, maybe N's)
   * //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:**

Genome Informatics