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bioRxiv · 10.64898/2026.07.28.741211

seqproc: An efficient, flexible, and concise tool for sequence geometry description and transformation

Cape, N.·Fisher, E.·Liu, D.·Patro, R.
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Abstract

Complex sequencing protocols encode technical information in read structure and require accurate, e[ff]icient preprocessing. We introduce seqproc, which compiles concise sequence-geometry descriptions into execution graphs. Across four single-cell RNA-sequencing protocols, seqproc has the lowest mean runtime at every tested thread count and uses substantially less memory than the next-fastest tool. It has the highest F1 agreement with conservative structural references on all three discriminative chemistries and ties both alternatives on the 10x length-filter control. By separating protocol description from execution, seqproc makes complex read transformations compact, reusable, and efficient.

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Cape, N., Fisher, E., Liu, D., Patro, R.. 2026-07-29. seqproc: An efficient, flexible, and concise tool for sequence geometry description and transformation. https://doi.org/10.64898/2026.07.28.741211

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