yuzhenpeng / steppingStone

A pipeline to identify chromothripsis breakpoints and trace cancer rearrangements

steppingStone v1.0

A pipeline to identify chromothripsis breakpoints and trace cancer rearrangements

Download and Compile:

$ git clone  https://github.com/wtsi-hpag/steppingStone.git 
$ cd steppingStone 
$ bash install.sh

If everything compiled successfully you must see the final comment: "Congrats: installation successful!"

External packages

The genome aligner BWA (https://github.com/lh3/bwa) and minimap2 (https://github.com/lh3/minimap2) are downloaded and compiled by steppingStone.

Run the pipelines

       $ /full/path/to/steppingStone/src/steppingStone -nodes <nodes>  \
             -reads /lustre/team117/zn1/project/cancer/PacBio-HiFi-sample.fastq.gz \
             reference.fasta breakpoints.dat  

   Note: "-reads " expects a full path or a file in the working directory.