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SPRING2 CLI Reference

This page lists the main command-line options by mode.

General Syntax

Compression:

spring2 -c --R1 <input_R1> [--R2 <input_R2>] [--R3 <input_R3>] [--I1 <input_I1>] [--I2 <input_I2>] [-o <archive.sp>]

Decompression:

spring2 -d -i <archive.sp> [-o <outputs...>] [--unzip]

Preview:

spring2 --preview -i <archive.sp> [--audit]

General Options

  • -h, --help: show command-line help
  • -V, --version: print version information
  • -o, --output <arg>: output archive or restored output path(s)
  • -t, --threads <arg>: number of worker threads
  • -m, --memory <arg>: approximate memory budget in GB; 0 disables the limit
  • -v, --verbose [info|debug]: logging level

Compression Options

  • -c, --compress: compression mode
  • -R1, --R1 <arg>: required read-1 input
  • -R2, --R2 <arg>: optional read-2 input; enables paired-end mode
  • -R3, --R3 <arg>: optional read-3 input; requires --R2
  • -I1, --I1 <arg>: optional index-read-1 input; currently requires --R2
  • -I2, --I2 <arg>: optional index-read-2 input; requires --I1
  • -l, --level <arg>: compression level 1..9
  • -s, --strip <arg>: discard one or more of i, o, q
  • -q, --qmod ...: quality storage mode
  • -n, --note <arg>: store a custom note in archive metadata
  • -y, --assay <arg>: select assay mode
  • -b, --cb-len <arg>: cellular barcode length for eligible single-cell assays
  • -a, --audit: run post-compression verification

Decompression Options

  • -d, --decompress: decompression mode
  • -i, --input <arg>: input archive path
  • -u, --unzip: force plain-text output even if the original input was gzipped

Preview Options

  • -p, --preview: inspect archive metadata without writing outputs
  • -i, --input <arg>: input archive path
  • -a, --audit: perform full in-memory archive integrity audit

Quality Mode Forms

  • -q lossless
  • -q qvz <qv_ratio>
  • -q ill_bin
  • -q binary <thr> <high> <low>

Assay Choices

  • auto
  • dna
  • rna
  • atac
  • bisulfite
  • sc-rna
  • sc-atac
  • sc-bisulfite

Output Naming Notes

  • For grouped archives, -o prefix expands to lane-specific suffixes such as .R1, .R2, .R3, .I1, and .I2.
  • For paired-end decompression, multiple output names can be passed explicitly.
  • If output names end in .gz, SPRING2 writes gzipped restored output.

See Also