RunDrap runtimes
All runs were performed with the Docker image sigenae/drap1.91 on a computer with 64G of RAM and 8 CPU's. The assembled dataset is the Dr dataset described in the DRAP publication. This dataset includes five Danio rerio public libraries (SRR1048059, SRR1048060, SRR1048061, SRR1048062, SRR1048063) for a total of approximately 40 million reads. RunDrap was launched with the following command lines on data previously trimmed and normalized.
runDrap --no-trim --no-norm --dbg-mem 60 -o SRR10480XX_oases \ --R1 SRR1048059_1.trim.norm.fq.gz SRR1048060_1.trim.norm.fq.gz SRR1048061_1.trim.norm.fq.gz \ SRR1048062_1.trim.norm.fq.gz SRR1048063_1.trim.norm.fq.gz \ --R2 SRR1048059_2.trim.norm.fq.gz SRR1048060_2.trim.norm.fq.gz SRR1048061_2.trim.norm.fq.gz \ SRR1048062_2.trim.norm.fq.gz SRR1048063_2.trim.norm.fq.gz runDrap --no-trim --no-norm --dbg-mem 60 -o SRR10480XX_trinity --dbg trinity \ --R1 SRR1048059_1.trim.norm.fq.gz SRR1048060_1.trim.norm.fq.gz SRR1048061_1.trim.norm.fq.gz \ SRR1048062_1.trim.norm.fq.gz SRR1048063_1.trim.norm.fq.gz \ --R2 SRR1048059_2.trim.norm.fq.gz SRR1048060_2.trim.norm.fq.gz SRR1048061_2.trim.norm.fq.gz \ SRR1048062_2.trim.norm.fq.gz SRR1048063_2.trim.norm.fq.gz