FAQ

The results of the first round partition are unsatisfactory.

In our two-round partition algorithm, the first round partition depends on the h-trans errors between homologous chromosomes; if you input a contig assembly with low level switch errors or input a high accuracy pore-c data, the h-trans will be not enough to cluster all contigs to correct homologous groups, resulting in unsatisfactory results. You can set the -q1 0 for hyperpartition to increase the rate of h-trans errors. However, this parameter may raise error of out of memory when you input huge pore-c data in porec table or hic contacts in pairs file.

How to set the -n parameter when assembling an aneuploid genome.

The aneuploid genome, such as modern cultivated sugarcane, contains unequal homologous chromosomes. The -n parameter can be set to zero (-n 10:0) to automatically partition contigs into different chromosomes within a homologous group.
However, we also allow the user to input a file with two columns: the first column is the index(1-base) of the first round partition, and the second column is the chromosome number of each homologous. And then specified the -n 10:second.number.tsv in cphasing pipeline or cphasing hyperpartition. - second.number.tsv

1    13
2    12
3    12
4    11
5    10
6    12
7    12
8    10
9    12
10    12