python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Anteholosticha_monilata-single-cell-SRR6339725/SRR6339725.read1.paired.fastq.gz --pe1-2 Anteholosticha_monilata-single-cell-SRR6339725/SRR6339725.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Anteholosticha_monilata-single-cell-SRR6339725
python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Bursaria_truncatella_CBSC-SRR7508180/SRR7508180.read1.paired.fastq.gz --pe1-2 Bursaria_truncatella_CBSC-SRR7508180/SRR7508180.read2.paired.fastq.gz --pe2-1 Bursaria_truncatella_CBSC-SRR7508181/SRR7508181.read1.paired.fastq.gz --pe2-2 Bursaria_truncatella_CBSC-SRR7508181/SRR7508181.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Bursaria_truncatella_CBSC-SRR7508181
python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Chilodonella_uncinata-SRR6195042/SRR6195042.read1.paired.fastq.gz --pe1-2 Chilodonella_uncinata-SRR6195042/SRR6195042.read2.paired.fastq.gz --pe2-1  Chilodonella_uncinata-SRR6195047/SRR6195047.read1.paired.fastq.gz --pe2-2 Chilodonella_uncinata-SRR6195047/SRR6195047.read2.paired.fastq.gz --pe3-1  Chilodonella_uncinata-SRR6195048/SRR6195048.read1.paired.fastq.gz --pe3-2 Chilodonella_uncinata-SRR6195048/SRR6195048.read2.paired.fastq.gz --pe4-1  Chilodonella_uncinata-SRR6195049/SRR6195049.read1.paired.fastq.gz --pe4-2 Chilodonella_uncinata-SRR6195049/SRR6195049.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Chilodonella_uncinata-SRR6195042
python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Colpoda_magna_ATCC_50128-SRR7458467/SRR7458467.read1.paired.fastq.gz --pe1-2 Colpoda_magna_ATCC_50128-SRR7458467/SRR7458467.read2.paired.fastq.gz  --pe2-1 Colpoda_magna_ATCC_50128-SRR7504389/SRR7504389.read1.paired.fastq.gz --pe2-2 Colpoda_magna_ATCC_50128-SRR7504389/SRR7504389.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Colpoda_magna_ATCC_50128-SRR7504389
python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Deviata_sp.-single-cell-SRR6339724/SRR6339724.read1.paired.fastq.gz --pe1-2 Deviata_sp.-single-cell-SRR6339724/SRR6339724.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Deviata_sp.-single-cell-SRR6339724
python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Diophrys_scutum-single-cell-SRR6339723/SRR6339723.read1.paired.fastq.gz --pe1-2 Diophrys_scutum-single-cell-SRR6339723/SRR6339723.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Diophrys_scutum-single-cell-SRR6339723
python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Halteria_grandinella-SRR8270648/SRR8270648.read1.paired.fastq.gz --pe1-2 Halteria_grandinella-SRR8270648/SRR8270648.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Halteria_grandinella-SRR8270648
python /oak/stanford/groups/akundaje/marinovg/programs/SPAdes-3.13.0-Linux/bin/spades.py -m 512 --plasmid --pe1-1 Heterometopus_sp.-60_hand-picked-cells-SRR6033281/SRR6033281.read1.paired.fastq.gz --pe1-2 Heterometopus_sp.-60_hand-picked-cells-SRR6033281/SRR6033281.read2.paired.fastq.gz -t 20 -o SPAdes-3.13-Heterometopus_sp.-60_hand-picked-cells-SRR6033281