This repository contains standards and pipelines for processing various assay and sequencing-platform data types. If you'd like to modify an existing workflow or contribute a new one please see the contribution guidelines.
- 10x-RNA-v2: 10x Genomics single-cell RNA-seq v2
- 10x-RNA-v3: 10x Genomics single-cell RNA-seq v3
- 10x-RNA-ATAC: 10x Genomics Multiome (single-cell RNA/ATAC)
- 10xCRISPR: 10x Genomics CRISPR and RNA-seq (single-cell RNA/CRISPR)
- CEL-Seq: barcoding and pooling samples before amplifying RNA with in vitro transcription (v1)
- CEL-Seq2: Improvement CEL-Seq, now with UMIs! Implemented on Fluidigm's C1 (v2)
- Quartz-seq: Riken technology for single-cell RNA-seq
- Quartz-seq2: Added umis to Quartz-seq (v2)
- SHARE-seq: combinatorial indexing stratgy for RNA + chromatin accessibility
- STRT-seq: single-cell tagged reverse transcripton
- STRT-seq-2i: STRT-seq performed on microwells with dual-index 5 prime
- STRT-seq-C1: STRT-seq performed on microfluidics Fluidigm C1
- Smart-seq2: full-length rna-seq from individual cells
- Smart-seq3: full-length and five-prime RNA-seq from individual cells
- sci-RNA-seq: combinatorial single-cell RNA-seq
Each assay contains:
README.mdwith details on
- Inputs
- Preprocessing tools
- Preprocessing steps
- Outputs
- Metrics (and their utility)
spec.mdwith the assay sequencing library specification (defined withseqspec)example.ipynba Google Colab notebook executing the atomic workflow
Todo: add contributions and citations as well as references (in the README.md) to the the workflow components.
Each sequencing company contains a README.md with details on
- Platforms produced by the company
- Platform specific concerns
- Methods for transforming platform specific files to FASTQs