PlasmaCNA provides a toolkit for analyzing tumor-derived copy number changes using low pass whole-genome sequencing of plasma cell-free DNA.
- Ability to generate and analyze both fixed size windows (ichorCNA, tMAD) and variable sized windows (PlasmaSeq)
- A set of functions for window read depth normalization
- A julia implementation of the PlasmaSeq algorithm
If PlasmaCNA is used in published research, please cite:
Favaro, Patricia F., et al. Feasibility of circulating tumor DNA analysis in dogs with naturally-occurring malignant and benign splenic lesions. (2022) Scientific Reports doi:10.1038/s41598-022-09716-6
Publications using the PlasmaSeq implementation provided in PlasmaCNA should also cite:
Farris, C., Trimarchi, J.M. Plasma-seq: a novel strategy for metastatic prostate cancer analysis. Genome Med 5, 35 (2013). https://doi.org/10.1186/gm439
Julia package dependencies are handled by the julia package manager, except QuickArgParse
https://github.com/brmcdonald/QuickArgParse
The R package DNACopy is used by the PlasmaSeq implementation for segmentation
GenMap is required for calculating mappability:
https://github.com/cpockrandt/genmap
The primary workflows are provided in the /bin directory of the package, with inputs specified in their usage statements.
fixbin_generation.jl
Generates a table of fixed size windows across the genome,
annotated with GC content and average mappability. Used by ichorCNA and other methods.
flexbin_generation.jl
Generates a table of windows across the genome such that each has approximately the
same number of mappable bases. Windows are annotated with GC content and average mappability.
Used by PlasmaSeq.
plasmaseq.jl
An implementation of the PlasmaSeq method for identifying large tumor-derived copy number changes.
The original PlasmaSeq implementation can be found here: https://github.com/PeterUlz/PlasmaSeq
genmap index -F /path/to/refgenome.fna -I genmap.index
genmap -K 50 -E 1 -w -T $NumCores -I genmap.index -O genmap.k50.e1.wig