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, 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 hic.mrege.pairs.pqs -t 40 -n 0:0 -hcr -p AAGCTT 
  

• Or add --merge-use-allele parameter to use the allelic contig pairs information to help the merging of homologous chromosomes in first-round cluster.

  cphasing pipeline -f sh_hifi.bp.p_utg.fasta -pct porec.mrege.porec.gz -t 40 -n 10:0 -hcr -p AAGCTT --merge-use-allele