https://github.com/alexpreynolds/kmer-counter-unordmap
Count canonical kmers with STL unordered_map
https://github.com/alexpreynolds/kmer-counter-unordmap
bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count
Last synced: about 1 month ago
JSON representation
Count canonical kmers with STL unordered_map
- Host: GitHub
- URL: https://github.com/alexpreynolds/kmer-counter-unordmap
- Owner: alexpreynolds
- Created: 2018-11-04T12:24:31.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2018-11-04T13:45:22.000Z (over 6 years ago)
- Last Synced: 2025-02-17T16:38:53.832Z (4 months ago)
- Topics: bioinformatics, cpp, hash-tables, kmer, kmer-counting, kmer-frequency-count
- Language: C++
- Size: 15.6 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# kmer-counter-unordmap
The `kfs` program reads in multiline FASTA records, counts canonical kmers using the STL `unordered_map`, 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}
...
```