kmerhash

Fast generation of hashed kmers from a python string

Installation

To install, wheels are available for Python >= 3.7 < 3.10 on linux/MacOSX:

pip install kmerhash

Or build from source:

git clone https://github.com/kcleal/kmerhash
cd kmerhash
pip install .

Overview

kmers are packed into an int64 using a rolling hash. The maximum kmer size is 32 bp and currently an alphabet of {A, T, C, G} is supported (uppercase only):

import numpy as np
from kmerhash import kmerhasher, hashes2seq

seq = "TTCGGACCGGATT"
k = 11
a = kmerhasher(seq, k)  # numpy array returned

print(a)
# [4039016 3573155 1709711]

kmer integers can be converted back to string format:

print(hashes2seq(a, k))
# ['TTCGGACCGGA', 'TCGGACCGGAT', 'CGGACCGGATT']

kmers can be counted efficiently using e.g. `Counter`:

from collections import Counter

counter = Counter(a)

Benchmarks

kmerhash was compared to a pure python implementation with k=21:

# pure python
[hash(seq[i:i+k]) for i in range(len(seq) - k + 1)]

# kmerhash
kmerhasher(seq, k)

Sequence length	Throughput python (Mbp / s)	Throughput kmerhash (Mbp / s)
21	9.8	1.1
100	5.6	9.1
1000	5.2	50.5
10,000	4.8	90.79
100,000	4.9	102.9

Limitations

• Maximum kmer length is 32
• Only {A, T, C, G} bases are supported
• Uppercase bases only
• N bases will be intepreted as A's

Acknowledgements

Alexander Kearsey https://github.com/kearseya