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https://github.com/alexpreynolds/kmer-counter-ska
Count canonical kmers with Malte Skarupke's bytell_hash_map hash table
https://github.com/alexpreynolds/kmer-counter-ska
bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: 8 days ago
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Count canonical kmers with Malte Skarupke's bytell_hash_map hash table
- Host: GitHub
- URL: https://github.com/alexpreynolds/kmer-counter-ska
- Owner: alexpreynolds
- Created: 2018-11-03T13:12:49.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2018-11-03T13:30:15.000Z (about 6 years ago)
- Last Synced: 2024-11-07T00:24:17.203Z (about 2 months ago)
- Topics: bioinformatics, cpp, hash-tables, kmer, kmer-counting, kmer-frequency-count
- Language: C++
- Size: 23.4 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# kmer-counter-ska
The `kfs` program reads in multiline FASTA records, counts canonical kmers using Malte Skarupke's [`bytell_hash_map` hash table](https://probablydance.com/2018/05/28/a-new-fast-hash-table-in-response-to-googles-new-fast-hash-table/), and measures time taken to read in and process records.
## Usage
### Compilation
```
$ make kfs
```### Performance
Specify variables `K` (integer) and `FASTA` (path to FASTA sequences).
```
$ /usr/bin/time -l ./kfs -k ${K} -i ${FASTA}
...
```