Igor Martayan

@imartayan.bsky.social

818 Followers 360 Following

PhD student in algorithmic bioinformatics at @bonsaiseqbioinfo.bsky.social. Interested in space-efficient data structures, sketching algorithms & high-performance computing https://igor.martayan.org

A pack of stickers with the logo of our new tool, K-mer Fast Counter a.k.a. KFC
Overview of the vectorized computation of minimizers. The sequence is first split into L chunks that are processed in parallel. The bases of each chunk are gathered in a SIMD register and passed to a vectorized rolling hash function that computes a hash for the k-mers in each lane. The position of the minimum is then computed over a sliding window of w vectors of hashes. The positions are finally reordered and deduplicated to have a unique occurrence of each position.