Scaffolding with scaffhic:

1. HiC pairs are aligned against the target assembly using BWA mem with a tag -5SPM for HiC reads;

2. PCR duplications and other artefacts are screened and removed from further data processing;

3. Based on read distributions, Contig Distance Index (CDI) is used to quantify the likelihood of contig joins;

4. Order and orientation are determined by pair numbers on contigs;

5. Relation matrix and partner matrix are used to reduce join errors;

6. Iterations are carried out for genome scaffolding;

7. Contigs are arranged into a scaffolding structure;

8. Distributions of HiC insert mapping sizes are plotted as a png image file;

9. HiC map is produced based on the scaffolded assembly


Sanger Contributors
External Contributors

Tool Type