A Snakemake workflow for calling somatic SNVs, fusions, and CNAs in high-quality long-read single-cell RNA-seq cancer samples, and infer subclonal structures based on those variants.
LongSom takes a bam file and a barcodes file as input. Before calling variants, it performs a cell types reannotation step for improved results. For more informations about the methods, please read our publication Dondi et al. 2024.
For more information, including installation and usage, please visit our Wiki.
If you use LongSom, please cite:
Arthur Dondi, Nico Borgsmüller, Pedro Ferreira, Brian Haas, Francis Jacob, Viola Heinzelmann-Schwarz, Tumor Profiler Consortium, Niko Beerenwinkel. De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data. bioRxiv
In addition, please cite SComatic if you use LongSom for SNV detection, CTAT-LR-fusion for fusion detection, and BnpC for subclonal structure reconstruction.