This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch.
To use the latest version, first run the following commands:
cd SALSA
make
To run the code, you will need Python 2.7, BOOST libraries and Networkx(version lower than 1.2).
If you consider using this tool, please cite our publication which describes the methods used for scaffolding.
Ghurye, J., Pop, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link
Ghurye, J., Rhie, A., Walenz, B.P., Schmitt, A., Selvaraj, S., Pop, M., Phillippy, A.M. and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p.261149 Link
For any queries, please either ask on github issue page or send an email to Jay Ghurye (jayg@cs.umd.edu).
