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PreprintCC BY-NC-NDbioRxiv

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

  • N. Cape
  • E. Fisher
  • D. Liu
  • R. Patro1
  1. 1University of Maryland
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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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Cite

BibTeXRIS
BibTeX
@misc{cape2026seqproc,
  title = {{seqproc: An efficient, flexible, and concise tool for sequence geometry description and transformation}},
  author = {N. Cape and E. Fisher and D. Liu and R. Patro},
  howpublished = {bioRxiv},
  year = {2026},
  month = jul,
  doi = {10.64898/2026.07.28.741211},
  url = {https://www.biorxiv.org/content/10.64898/2026.07.28.741211v2},
  note = {CC BY-NC-ND},
}
RIS
TY  - UNPB
TI  - seqproc: An efficient, flexible, and concise tool for sequence geometry description and transformation
AU  - N. Cape
AU  - E. Fisher
AU  - D. Liu
AU  - R. Patro
PY  - 2026
DA  - 2026/07/28
PB  - bioRxiv
DO  - 10.64898/2026.07.28.741211
UR  - https://www.biorxiv.org/content/10.64898/2026.07.28.741211v2
AB  - 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.
ER  -