N. Cape, E. Fisher, D. Liu, R. Patro
We introduce seqproc, a general-purpose sequence pre-processing tool based on a concise descriptive grammar to specify sequence matching and transformations. seqproc compiles a user-provided sequence geometry and transformation description into an execution graph, executed by the antisequence library. We demonstrate that seqproc is faster on most chemistries, substantially more memory efficient, and at least as accurate as alternative tools that provide similar functionality, while having a more concise description syntax.
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.