Platanus

 Platanus_trim xxx_1.fastq xxx_2.fastq

 Platanus assemble -o Pxut -f ./DRR02167[34]_[12].fastq 2> assemble.log

Platanus scaffold -o Pxut -c Pxut_contig.fa -b Pxut_contigBubble.fa -IP1 ./DRR021673_1.fastq ./DRR021673_2.fastq –IP2 ./DRR021674_1.fastq ./DRR021674_2.fastq -OP3 ./DRR021675_1.fastq ./DRR021675_2.fastq ./DRR021676_1.fastq ./DRR021676_2.fastq 2> scaffold.log

 

Platanus gap_close -o Pxut -c Pxut_scaffold.fa -IP1 ./DRR021673_1.fastq ./DRR021673_2.fastq –IP2 ./DRR021674_1.fastq ./DRR021674_2.fastq -OP3 ./DRR021675_1.fastq ./DRR021675_2.fastq ./DRR021676_1.fastq ./DRR021676_2.fastq 2> gapclose.log