SPRING2 User Documentation¶

This directory contains the end-user handbook for building, running, and inspecting SPRING2 archives.

Start Here¶

Installation Guide: prebuilt binaries, installers, and platform-specific install notes.
Building Overview: prerequisites, build strategy, and links to platform-specific build commands.
Usage Overview: quick-start examples and a map of the runtime guides.

Platform Build Commands: Linux, macOS, and Windows build recipes.
Compression Guide: input layouts, grouped lanes, performance tuning, and archive creation examples.
End-to-End Examples: complete command sequences for common assay workflows and grouped-lane pipelines.
Decompression Guide: output naming, gzip behavior, grouped archive restoration, and verification behavior.
Archive Inspection: preview mode, archive auditing, notes, gzip metadata, and what preview output means.
Assays and Quality Modes: assay selection, assay-aware transforms, barcode handling, lossy modes, and --strip.
CLI Reference: option-by-option command reference.

Assay Reference Construction: technical background on the assay-detection reference.
Development Guide: contributor and maintenance documentation.