https://github.com/alexpreynolds/kmer-counter-sparse
Count canonical kmers with Google sparse_hash_map
Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
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○Scientific vocabulary similarity
Low similarity (2.9%) to scientific vocabulary
Keywords
Repository
Count canonical kmers with Google sparse_hash_map
Basic Info
- Host: GitHub
- Owner: alexpreynolds
- Language: C++
- Default Branch: master
- Size: 5.86 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
kmer-counter-sparse
The kfs program reads in multiline FASTA records, counts canonical kmers using Google's sparse_hash_map hash table, and measures time taken to read in and process records.
Usage
To install sparse_hash_map libraries on OS X, use Homebrew: brew install google-sparsehash.
Compilation
$ make kfs
Performance
Specify variables K (integer) and FASTA (path to FASTA sequences).
$ /usr/bin/time -l ./kfs -k ${K} -i ${FASTA}
...
Owner
- Name: Alex Reynolds
- Login: alexpreynolds
- Kind: user
- Location: Seattle, WA USA
- Company: Altius Institute for Biomedical Sciences
- Website: bitsumma.com
- Repositories: 92
- Profile: https://github.com/alexpreynolds
Pug caregiver, curler, cyclist, gardener, beginning French scholar
GitHub Events
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Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Alex Reynolds | a****s@g****m | 2 |
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Last synced: 9 months ago
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