https://github.com/alexpreynolds/kmer-counter-ska
Count canonical kmers with Malte Skarupke's bytell_hash_map hash table
Science Score: 13.0%
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○CITATION.cff file
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○Scientific vocabulary similarity
Low similarity (2.6%) to scientific vocabulary
Keywords
bioinformatics
cpp
hash-tables
kmer
kmer-counting
kmer-frequency-count
Last synced: 6 months ago
·
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Repository
Count canonical kmers with Malte Skarupke's bytell_hash_map hash table
Basic Info
- Host: GitHub
- Owner: alexpreynolds
- Language: C++
- Default Branch: master
- Size: 23.4 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
bioinformatics
cpp
hash-tables
kmer
kmer-counting
kmer-frequency-count
Created over 7 years ago
· Last pushed over 7 years ago
Metadata Files
Readme
README.md
kmer-counter-ska
The kfs program reads in multiline FASTA records, counts canonical kmers using Malte Skarupke's bytell_hash_map 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}
...
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 | 4 |
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Last synced: 9 months ago
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Past Year
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- Average comments per issue: 0
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- Bot issues: 0
- Bot pull requests: 0