PATHS
JELLYFISH_PATH=/storage/acestorage/software/MaSuRCA-2.0.3.1/bin
SR_PATH=/storage/acestorage/software/MaSuRCA-2.0.3.1/bin
CA_PATH=/storage/acestorage/software/MaSuRCA-2.0.3.1/CA/Linux-amd64/bin
END

DATA
PE= pe RUNNER_PARAM_INSERT_SIZE RUNNER_PARAM_DEVIATION RUNNER_PARAM_LEFT RUNNER_PARAM_RIGHT
JUMP= sh RUNNER_PARAM_MP_INSERT_SIZE RUNNER_PARAM_MP_DEVIATION RUNNER_PARAM_MP_LEFT RUNNER_PARAM_MP_RIGHT
END

PARAMETERS
GRAPH_KMER_SIZE=RUNNER_PARAM_K
USE_LINKING_MATES=1
LIMIT_JUMP_COVERAGE = 60
CA_PARAMETERS = ovlMerSize=30 cgwErrorRate=0.25 ovlMemory=4GB
KMER_COUNT_THRESHOLD = 1
NUM_THREADS=RUNNER_PARAM_THREADS
JF_SIZE=3500000000
DO_HOMOPOLYMER_TRIM=0
END
