Scaffolding with HiC data

This workflow perfoms scaffolding using HiC data with YAHS. It is designed to be run as part of one the VGP analysis trajectories. Example of trajectory :

• VGP1 : Kmer profiling
• VGP4 : Genome assembly with HiC phasing
• VGP6 : Purge duplicated haplotigs
• VGP8 : Scaffolding with HiC

Inputs

1. Scaffolded assembly [fasta]
2. Concatenated HiC forward reads [fastq]
3. Concatenated HiC reverse reads [fastq]
4. Restriction enzyme sequence [txt]
5. Estimated genome size [txt]

Outputs

1. Scaffolds in [fasta] and [gfa] format
2. QC: Assembly statistics
3. QC: Nx plot
4. QC: Size plot
5. QC: BUSCO report
6. QC: Pretext Maps before and after scaffolding