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Single-Cell RNA / ATAC Sequencing

Domain key: single-cell

Single-cell sequencing resolves gene expression or chromatin accessibility at the individual cell level. Codaris supports 10x Genomics scRNA-seq and scATAC-seq workflows, with open-source alternatives to CellRanger.

Step Tool Notes
QC FastQC Raw read quality
Counting (10x) CellRanger Industry standard for 10x data
Counting (open) STARsolo Open-source, nf-core native
Counting (fast) alevin-fry Fastest pseudo-alignment option
Downstream Seurat / Scanpy R / Python analysis (outside pipeline scope)

Best Practices Enforced

  • CellRanger is the default for 10x Genomics — alevin-fry or STARsolo can be substituted if requested
  • Empty droplet filtering (emptyDrops or CellRanger's built-in filter) is enforced before any count matrix is output
  • Doublet detection (DoubletFinder, scrublet) is flagged as a required downstream step — Codaris will remind you even if it's outside the Nextflow scope
  • Cell barcode whitelists must be provided for custom protocols; 10x whitelists are bundled with CellRanger

Example Prompts

Build a 10x Genomics scRNA-seq pipeline for human PBMCs,
GRCh38 genome, CellRanger counting

codaris > I want an open-source scRNA-seq pipeline — no CellRanger licence.
          Use STARsolo for counting. 10x Chromium v3 chemistry.

Build a scATAC-seq pipeline for 10x Multiome data.
I need fragment files and peak matrix output.

codaris > Check my STARsolo parameters — am I using the right
          barcode whitelist for 10x Chromium v3?