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 genome, containing unequal numbers of chromosomes across homologous groups. Therefore, we set -n 10:0 to automatically determine the number of clusters.

To rescue collapsed regions, enable CollapseRescue by providing the assembly graph with --collapsed-rescue --gfa sh_hifi.bp.p_utg.no_seq.gfa, allowing collapsed unitigs to be identified and reassigned.

Optionally, the --refine parameter can be enabled to further reduce inter-homologous misassignments and improve phasing accuracy. Optionally, the -x very-sensitive parameter can be enabled for fragmented assemblies (HiFi-only) or low-depth sequencing data.

cphasing pipeline -f sh_hifi.bp.p_utg.fasta -pct porec.mrege.porec.gz -t 40 -n 10:0 -hcr -p AAGCTT --collapsed-rescue --gfa sh_hifi.bp.p_utg.no_seq.gfa