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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
  • 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