Assemble hybrid sugarcane by Pore-C

Aneuploidy (2n=114), estimate genome size ~ 10 Gb

Pore-C data processing

Due to the huge porec data, we mapped each cell to fasta by submitting this command to cluster, respectively. And merged them into one file by cphasing porec-merge

cphasing mapper sh_hifi.bp.p_utg.fasta porec-1.fastq.gz -t 40 
cphasing mapper sh_hifi.bp.p_utg.fasta porec-2.fastq.gz -t 40 
cphasing mapper sh_hifi.bp.p_utg.fasta porec-3.fastq.gz -t 40 
cphasing mapper sh_hifi.bp.p_utg.fasta porec-4.fastq.gz -t 40 
cphasing mapper sh_hifi.bp.p_utg.fasta porec-5.fastq.gz -t 40 

cphasing porec-merge porec-*.porec.gz -o porec.merge.porec.gz 

Assembling by cphasing pipeline

Modern hybrid sugarcane is an aneuploid, which contains an unequal number of chromosomes in each homologous group, so we set -n 0:0 to automatically output cluster numbers.

cphasing pipeline -f sh_hifi.bp.p_utg.fasta -pct porec.mrege.porec.gz -t 40 -n 0:0 -hcr -p AAGCTT