!!! under construction !!!
SCM-seq (Single-Cell and -Molecule sequencing) is an integrated platform that enables single-cell multiomic analysis by combining high-throughput scRNA-seq to Oxford Nanopore Technologies (ONT) single-molecule sequencing.
In particular, SCM-seq allows to explore and link distinct sources of intratumor heterogeneity on each individual cell:
- Expressed somatic variants
- Gene expression
- Splicing isoforms
This repo collects state-of-the-art scripts and pipelines for pre-processing and downstream analyses developed within the SRSF2-AML project.
For the time being, the workflow includes the following steps (order is mandatory):
- scRNA-seq
- Cell barcode (CB) matching
- Long-read alignment and annotation
- Mutation analysis and genotype assignment
- Target enrichment quality check
- Genotype analysis
- Isoform analysis
Steps 2-5 are enclosed into a dedicated Snakemake workflow.