Introduction
seqproc turns a declarative read geometry into an executable FASTQ
preprocessing graph. It is designed for protocols in which useful sequence is
distributed among fixed positions, variable intervals, linker-delimited
regions, and one or more read orientations.
The project has two deliberately separate layers:
- The Extended Fragment Geometry Description Language (EFGDL) describes the input layout and desired output.
- The ANTISEQUENCE execution backend performs matching, filtering, extraction, rewriting, and FASTQ I/O.
That separation makes a geometry inspectable and reusable without tying it to
a shell pipeline or protocol-specific program. seqproc validate catches
syntax and semantic errors before processing; seqproc explain shows the
normalized description and compiled graph.
Suitable workloads
Section titled “Suitable workloads”seqproc is particularly useful when a workflow needs one or more of:
- fixed or variable-length barcode and UMI extraction;
- anchor searches with Hamming or edit-distance tolerance;
- whitelist filtering and barcode replacement;
- forward, reverse, or either-orientation matching;
- explicit handling of equal-best barcode matches;
- paired-end transformations and demultiplexed output;
- bounded multithreading, compressed input/output, or preserved read order;
- machine-readable processing summaries.
It is not a read aligner, basecaller, cell caller, or quantifier. Its output is FASTQ prepared for those downstream tools.
Project status
Section titled “Project status”seqproc is under active development alongside the
seqproc preprint.
The command-based CLI (validate, explain, and run) is the preferred
interface. A legacy flag-only invocation remains temporarily available for
compatibility.
The language’s normative reference is the independent
EFGDL specification. This site focuses on
the currently implemented seqproc interface and practical use.