Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

1. Hifi long reads [fastq]
2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
4. K-mer database [meryldb]
5. Genome profile summary generated by Genomescope [txt]
6. Name of first assembly
7. Name of second assembly

Outputs

1. Haplotype 1 assembly ([fasta] and [gfa])
2. Haplotype 2 assembly ([fasta] and [gfa])
3. QC: BUSCO report for both assemblies
4. QC: Merqury report for both assemblies
5. QC: Assembly statistics for both assemblies
6. QC: Nx plot for both assemblies
7. QC: Size plot for both assemblies