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bioRxiv · 10.64898/2026.03.26.714584

A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers

Durbin, R.
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Abstract

Skiplists (Pugh, 1990) are probabilistic data structures over ordered lists supporting [O] (log N) insertion and search, which share many properties with balanced binary trees. Previously we introduced the graph Burrows-Wheeler transform (GBWT) to support efficient search over pangenome path sets, but current implementations are static and cumbersome to build and use. Here we introduce a doubly-linked skiplist variant over run-length-compressed BWTs that supports [O] (log N) rank and access operations, and a dynamic version of this that supports [O] (log N + S) rank and insert operations, where S is the number of symbols in the alphabet. We use these to store and search over paths through a syncmer graph built from Edgars closed syncmers, equivalent to a sparse de Bruijn graph. Code is available in rskip.[ch] within the syng package at github.com/richarddurbin/syng. This builds a 5.8 GB lossless GBWT representation of 92 full human genomes, single-threaded in 52 minutes, on top of a 4GB 63bp syncmer set built in 37 minutes. Arbitrarily long maximal exact matches (MEMs) can then be found as seeds for sequence matches to the graph at a search rate of approximately 1Gbp per 10 seconds per thread.

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Durbin, R.. 2026-03-29. A run-length-compressed skiplist data structure for dynamic GBWTs supports time and space efficient pangenome operations over syncmers. https://doi.org/10.64898/2026.03.26.714584

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