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

Count canonical kmers with Emil Ernerfeldt's emilib::HashMap
https://github.com/alexpreynolds/kmer-counter-emilib

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

Last synced: 8 days ago
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Count canonical kmers with Emil Ernerfeldt's emilib::HashMap

• Host: GitHub
• URL: https://github.com/alexpreynolds/kmer-counter-emilib
• Owner: alexpreynolds
• Created: 2018-11-04T13:02:26.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2018-11-04T13:04:26.000Z (about 6 years ago)
• Last Synced: 2024-11-07T00:24:17.600Z (about 2 months ago)
• Topics: bioinformatics, cpp, hash-tables, kmer, kmer-counting, kmer-frequency-count
• Language: C++
• Size: 10.7 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# kmer-counter-emilib

The `kfs` program reads in multiline FASTA records, counts canonical kmers using Emil Ernerfeldt's [`emilib::HashMap` hash table](https://github.com/emilk/emilib/blob/master/emilib/hash_map.hpp), and measures time taken to read in and process records. A discussion about performance characteristics compared with the C++ STL `std::unordered_map` is [available from the author](http://www.ilikebigbits.com/blog/2016/8/28/designing-a-fast-hash-table).

## Usage

### Compilation

```

$ make kfs

```

### Performance

Specify variables `K` (integer) and `FASTA` (path to FASTA sequences).

```

$ /usr/bin/time -l ./kfs -k ${K} -i ${FASTA}

...

```