Rename

Rename and reorient the chromosome, according to a monoploid or closely relative species's genome.

Rename phased assembly from phasing mode

The phasing mode of C-Phasing has been clustering the chromsomes into the same homologous and oriented them to parallel.

cphasing rename -r mono.fa -f draft.asm.fasta -a groups.agp -t 20 

Rename all of the chromosomes

Rename assembly from basal or basal_withprune mode, with the --unphased parameter.

cphasing rename -r mono.fa -f draft.asm.fasta -a groups.agp -t 20 --unphased 

Use the uppercase letter as the suffix of the chromosome name

Chr01A Chr01B Chr01C ...

cphasing rename -r mono.fa -f draft.asm.fasta -a groups.agp -t 20 -s upperletter