https://github.com/alexpreynolds/kmer-counter-sparse

Count canonical kmers with Google sparse_hash_map
https://github.com/alexpreynolds/kmer-counter-sparse

bioinformatics cpp hash-tables kmer kmer-counting kmer-frequency-count

Last synced: 8 days ago
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Count canonical kmers with Google sparse_hash_map

• Host: GitHub
• URL: https://github.com/alexpreynolds/kmer-counter-sparse
• Owner: alexpreynolds
• Created: 2018-11-03T13:57:51.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2018-11-03T14:23:19.000Z (about 6 years ago)
• Last Synced: 2024-11-07T00:24:16.248Z (about 2 months ago)
• Topics: bioinformatics, cpp, hash-tables, kmer, kmer-counting, kmer-frequency-count
• Language: C++
• Size: 5.86 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# kmer-counter-sparse

The `kfs` program reads in multiline FASTA records, counts canonical kmers using Google's [`sparse_hash_map` hash table](https://github.com/sparsehash/sparsehash), 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}

...

```