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SPRING2 Usage Guide

This page is the entry point for using SPRING2. The detailed task guides are split into smaller documents so common workflows are easier to find.

Quick Start

Compress paired-end FASTQ:

spring2 -c --R1 sample_1.fastq --R2 sample_2.fastq -o sample.sp

Decompress an archive:

spring2 -d -i sample.sp -o restored_1.fastq restored_2.fastq

Preview archive metadata without extracting:

spring2 --preview -i sample.sp

Audit an archive without writing decompressed FASTQ to disk:

spring2 --preview --audit -i sample.sp

Common Workflows

  • Compression Guide: creating archives from FASTQ or FASTA, grouped lanes, gzip input handling, performance knobs, and notes.
  • End-to-End Examples: complete command sequences for DNA, RNA, ATAC, bisulfite, and single-cell workflows.
  • Decompression Guide: restoring archives, choosing output names, gzip restoration rules, grouped outputs, and --unzip.
  • Archive Inspection: preview mode, audit mode, stored metadata, and gzip/BGZF reporting.
  • Assays and Quality Modes: assay selection, barcode-related behavior, lossy quality modes, and --strip.
  • CLI Reference: complete flag-by-flag option list.

Input Layouts

SPRING2 supports these main input patterns:

  • Single-end FASTQ or FASTA
  • Paired-end FASTQ or FASTA with --R1 and --R2
  • Grouped archives using optional --R3, --I1, and --I2
  • Plain-text and .gz inputs

When grouped lanes are present, a single archive can preserve the read pair, read-3 lane, and index lanes together.

Output Behavior Summary

  • Compression writes .sp archives.
  • Decompression uses the original input filenames when possible if you do not specify --output.
  • For grouped archives, -o prefix expands to prefix.R1, prefix.R2, and optional prefix.R3, prefix.I1, and prefix.I2.
  • For paired-end decompression, supplying one output base name can expand into two outputs when appropriate.

Logging and Verification

  • Default logging uses a concise progress display plus warnings and errors.
  • --verbose or --verbose info prints step-by-step informational logs.
  • --verbose debug enables detailed troubleshooting diagnostics.
  • Standard decompression already verifies stored record digests.
  • --audit adds a verification pass after compression, or performs a full dry-run integrity audit when used with --preview.