A Python library for counting short DNA sequences for use in Bioinformatics. DNA Hash stores k-mer sequence counts by their up2bit encoding - a two-way hash that works with variable-length sequences. DNA Hash uses considerably less memory than a lookup table that stores sequences in plaintext. In addition, DNA Hash's novel autoscaling Bloom filter eliminates the need to explicitly store counts for sequences that have only been seen once.

• Ultra-low memory footprint
• Embarrassingly parallelizable
• Open-source and free to use commercially

Note: The maximum sequence length is platform dependent. On a 64-bit machine, the max length is 31. On a 32-bit machine, the max length is 15.

Note: Due to the probabilistic nature of the Bloom filter, DNA Hash may over count sequences at a bounded rate.

• [1] https://github.com/JohnLonginotto/ACGTrie/blob/master/docs/UP2BIT.md.
• [2] P. Melsted et al. (2011). Efficient counting of k-mers in DNA sequences using a bloom filter.
• [3] S. Deorowicz et al. (2015). KMC 2: fast and resource-frugal k-mer counting.
• [4] A. DalPino. (2021). OkBloomer, a novel autoscaling Bloom Filter [link].