python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.11.1-Linux/bin/spades.py --pe1-1 SSBO1.read1.paired.fastq.gz --pe1-2 SSBO1.read2.paired.fastq.gz --trusted-contigs /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/sequence/symbB.v1.0.genome.fa -t 16 -o SSBO1-SPAdes-3.11.1-trimmed-with-contigs