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Assemble hybrid sugarcane by Hi-C

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

Hi-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 pairs-merge.

Note

Please submit one first; wait until the index is successfully created and the remaining jobs are enabled to submit to the cluster.

cphasing hic mapper -f sh_hifi.bp.p_utg.fasta -hic1 hic-1_R1.fastq.gz -hic2 hic-1_R2.fastq.gz -t 40 -k 27 -w 14 

cphasing hic mapper -f sh_hifi.bp.p_utg.fasta -hic1 hic-2_R1.fastq.gz -hic2 hic-2_R2.fastq.gz -t 40 -k 27 -w 14 
cphasing hic mapper -f sh_hifi.bp.p_utg.fasta -hic1 hic-3_R1.fastq.gz -hic2 hic-3_R2.fastq.gz -t 40 -k 27 -w 14 
cphasing hic mapper -f sh_hifi.bp.p_utg.fasta -hic1 hic-4_R1.fastq.gz -hic2 hic-4_R2.fastq.gz -t 40 -k 27 -w 14 

cphasing pairs-merge hic-*.pairs.pqs -o hic.merge.pairs.pqs

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.

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