Basic usage

Basic usage only requires the user to construct a single command, run ascat.pl to see the command line options. Running on a single core the analysis should complete in ~24 hours, however setting the -cpus option to 4 will drastically reduce the run-time of the early steps.

Docker

You need to mount all inputs (read only) and output (read-write) locations using the volume option (-v). In the example below $PWD can be replaced with any location, but the full path must be provided. Please see Docker documentation for further information on the volume option.

# this is a single multi-line command
docker run --rm -ti -v $PWD/input:/data/input:ro \
 -v $PWD/ref:/data/ref:ro \
 -v $PWD/output:/data/output:rw \
 quay.io/wtsicgp/ascatngs:4.5.0 \
  ascat.pl \
   -r /data/ref/genome.fa \
   -t /data/input/tumour.bam \
   -n /data/input/normal.bam \
   -o /data/output # ... other options