README.md

# YaHS: yet another Hi-C scaffolding tool [![DOI](https://zenodo.org/badge/411044095.svg)](https://zenodo.org/badge/latestdoi/411044095)

This is simple YaHS, for private use.

Use it with

    ./yahs example.gfa

Default output files are `yahs.fa` and `yahs.agp`.

The GFA file should contain `L` lines (`W` lines are silently discarded), and these tags set:

 - `S` lines should have the `LN:i:` tag set with the sequence length.
 - `L` lines should have the `FC:i:` tag set with a score.

## Original work

 - Citation: Chenxi Zhou, Shane A. McCarthy, Richard Durbin. YaHS: yet another Hi-C scaffolding tool. *Bioinformatics*, 39(1), btac808.
 - Repo: https://github.com/c-zhou/yahs