SPRING2 End-to-End Examples¶

This page collects complete command sequences for common assay pipelines. Each example shows a typical compression flow, optional inspection, and restoration command.

Conventions¶

Replace the example input filenames with your actual files.
sample.sp refers to the SPRING2 archive produced by compression.
restored refers to the output prefix used during decompression.

Paired-End DNA or WGS¶

Typical paired-end DNA datasets can use the default auto assay mode or an explicit dna setting when you want deterministic behavior.

spring2 -c \
  --R1 tumor_R1.fastq.gz \
  --R2 tumor_R2.fastq.gz \
  --assay dna \
  --threads 16 \
  --memory 16 \
  --note "sample=tumor01 assay=dna" \
  -o tumor01.sp

spring2 --preview -i tumor01.sp

spring2 -d -i tumor01.sp -o tumor01_restored_R1.fastq.gz tumor01_restored_R2.fastq.gz

Bulk RNA-seq¶

For bulk RNA-seq, use rna explicitly if you already know the assay, or keep auto if you want SPRING2 to classify the startup sample.

spring2 -c \
  --R1 rna_R1.fastq.gz \
  --R2 rna_R2.fastq.gz \
  --assay rna \
  --threads 12 \
  --note "project=atlas tissue=liver" \
  -o rna_liver.sp

spring2 --preview -i rna_liver.sp

spring2 -d -i rna_liver.sp -o rna_liver_R1.fastq.gz rna_liver_R2.fastq.gz

ATAC-seq¶

ATAC workflows benefit from explicit assay selection when you want predictable adapter-aware handling across repeated runs.

spring2 -c \
  --R1 atac_R1.fastq.gz \
  --R2 atac_R2.fastq.gz \
  --assay atac \
  --threads 12 \
  --note "sample=PBMC atac" \
  -o pbmc_atac.sp

spring2 --preview -i pbmc_atac.sp

spring2 --preview --audit -i pbmc_atac.sp

spring2 -d -i pbmc_atac.sp -o pbmc_atac_R1.fastq.gz pbmc_atac_R2.fastq.gz

Bisulfite Sequencing¶

Use the bisulfite assay mode when the reads come from bisulfite-converted DNA.

spring2 -c \
  --R1 bsseq_R1.fastq.gz \
  --R2 bsseq_R2.fastq.gz \
  --assay bisulfite \
  --threads 8 \
  --note "cohort=methylation batch=02" \
  -o methylation_batch02.sp

spring2 --preview -i methylation_batch02.sp

spring2 -d -i methylation_batch02.sp -o methylation_batch02_R1.fastq.gz methylation_batch02_R2.fastq.gz

Single-Cell RNA-seq with I1 Index Reads¶

When the cellular barcode is stored in I1, pass the grouped index lanes during compression. SPRING2 restores them as grouped outputs during decompression.

spring2 -c \
  --R1 scrna_R1.fastq.gz \
  --R2 scrna_R2.fastq.gz \
  --I1 scrna_I1.fastq.gz \
  --I2 scrna_I2.fastq.gz \
  --assay sc-rna \
  --threads 16 \
  --note "library=10x sample=donorA" \
  -o donorA_scrna.sp

spring2 --preview -i donorA_scrna.sp

spring2 -d -i donorA_scrna.sp -o donorA_scrna_restored

Expected grouped outputs:

donorA_scrna_restored.R1
donorA_scrna_restored.R2
donorA_scrna_restored.I1
donorA_scrna_restored.I2

Single-Cell RNA-seq with Barcode in R1¶

When no I1 lane exists and the cellular barcode is part of the R1 prefix, set --cb-len to the barcode length.

spring2 -c \
  --R1 scrna_R1.fastq.gz \
  --R2 scrna_R2.fastq.gz \
  --assay sc-rna \
  --cb-len 16 \
  --threads 16 \
  --note "library=dropseq cb=R1-prefix" \
  -o dropseq_scrna.sp

spring2 --preview -i dropseq_scrna.sp

spring2 -d -i dropseq_scrna.sp -o dropseq_scrna_R1.fastq.gz dropseq_scrna_R2.fastq.gz

Single-Cell ATAC-seq¶

Single-cell ATAC is typically paired-end and may also benefit from grouped lane handling depending on the upstream sequencer layout.

spring2 -c \
  --R1 scatac_R1.fastq.gz \
  --R2 scatac_R2.fastq.gz \
  --assay sc-atac \
  --threads 16 \
  --memory 24 \
  --note "sample=multiome01 modality=sc-atac" \
  -o multiome01_scatac.sp

spring2 --preview -i multiome01_scatac.sp

spring2 -d -i multiome01_scatac.sp -o multiome01_scatac_R1.fastq.gz multiome01_scatac_R2.fastq.gz

Single-Cell Bisulfite¶

Single-cell bisulfite datasets can use explicit assay selection and optional barcode handling in the same way as other single-cell assays.

spring2 -c \
  --R1 scbs_R1.fastq.gz \
  --R2 scbs_R2.fastq.gz \
  --assay sc-bisulfite \
  --cb-len 16 \
  --threads 12 \
  --note "assay=sc-bisulfite plate=P3" \
  -o plateP3_scbs.sp

spring2 --preview -i plateP3_scbs.sp

spring2 -d -i plateP3_scbs.sp -o plateP3_scbs_R1.fastq.gz plateP3_scbs_R2.fastq.gz

Grouped Read-3 plus Index Pipeline¶

Use grouped mode when the run includes paired reads plus read-3 and index lanes. Decompression restores all lanes from one archive.

spring2 -c \
  --R1 run_R1.fastq.gz \
  --R2 run_R2.fastq.gz \
  --R3 run_R3.fastq.gz \
  --I1 run_I1.fastq.gz \
  --I2 run_I2.fastq.gz \
  --assay sc-rna \
  --threads 16 \
  --note "grouped-lanes run=42" \
  -o run42_grouped.sp

spring2 --preview -i run42_grouped.sp

spring2 -d -i run42_grouped.sp -o run42_restored

Expected grouped outputs:

run42_restored.R1
run42_restored.R2
run42_restored.R3
run42_restored.I1
run42_restored.I2

FASTA Example¶

SPRING2 also supports FASTA input directly.

spring2 -c --R1 contigs.fasta -o contigs.sp

spring2 --preview -i contigs.sp

spring2 -d -i contigs.sp -o contigs_restored.fasta

Lossy Quality Example¶

This example keeps read sequences but compresses qualities using QVZ.

spring2 -c \
  --R1 reads_R1.fastq \
  --R2 reads_R2.fastq \
  --qmod qvz 1.0 \
  --assay dna \
  -o reads_lossy_qvz.sp

spring2 --preview -i reads_lossy_qvz.sp

Use lossy modes only when downstream requirements allow quality modification.

Verification-Focused Workflow¶

If the priority is archive validation for transfer or storage, combine compression-time audit and later preview-time audit.

spring2 -c \
  --R1 archive_R1.fastq.gz \
  --R2 archive_R2.fastq.gz \
  --audit \
  -o archival_copy.sp

spring2 --preview --audit -i archival_copy.sp