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https://github.com/alexpreynolds/kmer-counter
Count kmers with a more efficient (faster) hash table
https://github.com/alexpreynolds/kmer-counter
bioinformatics cpp14 genomics hash-map kmer kmer-counting
Last synced: about 21 hours ago
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Count kmers with a more efficient (faster) hash table
- Host: GitHub
- URL: https://github.com/alexpreynolds/kmer-counter
- Owner: alexpreynolds
- License: mit
- Created: 2017-01-31T21:15:32.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-06-08T04:09:33.000Z (5 months ago)
- Last Synced: 2024-06-08T05:24:19.251Z (5 months ago)
- Topics: bioinformatics, cpp14, genomics, hash-map, kmer, kmer-counting
- Language: C++
- Homepage:
- Size: 44.9 KB
- Stars: 24
- Watchers: 3
- Forks: 6
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# kmer-counter
Compilation
-----------
Run `make` to build the `kmer-counter` binary.
This has been compiled under Ubuntu 18.04.4, Cygwin 3.1.4, and Mac OS X 10.15.3, using concurrent GCC/glibc and Clang toolkits.
Usage
-----
Run `kmer-counter --help` for a list of options.
There are a couple ways to use this.
1. You can provide a single-line FASTA input and write counts to standard output, *e.g.*:
```
$ ./kmer-counter --fasta --k=6 sequences.fa
>foo CGTTAA:1 TTAACG:1
>bar TTCTTA:1 TAGGGC:1 AAATTC:1 GTGGAA:1 AACTTC:1 ...
...
```
2. For a more complex use case, you can provide a four-column BED file with the interval's genomic sequence in the fourth column (*i.e.*, ID field), along with the number *k* for the k-mers you want to count, an *offset* value for mer-keys (explained below), and a *results directory* to write results, *e.g.*:
```
$ ./kmer-counter --bed --k=6 --offset=12195 --results-dir="6mers" intervals.bed4
```
The above example generates 6-mers of the sequences from the file `intervals.bed4`.
The results are stored in a folder called `6mers`, which contains two files `count.bed` and `map.txt`.
The first file `count.bed` contains a BED file of intervals from `intervals.bed4`, where the fourth column contains a space-delimited pair of "mer"-keys and the number of times that key is seen. Mer-keys are numbers which begin at the `offset` value provided on the command-line.
The second file `map.txt` contains a tab-delimited pairing of mers and their mer-key, as found in `count.bed`.
Notes
-----
I am using a [hash table](https://en.wikipedia.org/wiki/Hash_table) implementation from [Emil Ernerfeldt](https://github.com/emilk/emilib/blob/master/emilib/hash_map.hpp). 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).