Socrates - SOft Clip re-alignment To idEntify Structural variants

Developed by Arthur Hsu, Jan Schroeder and Tony Papenfuss

Introduction

Socrates is a highly efficient and effective method for detecting genomic rearrangements in tumours that utilises split-read data. Socrates features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.

The latest version of Socrates (version 1.1+) is available from github. It requires Java 1.8. Older versions are also available. They will run with older versions of Java.

If you find Socrates useful, please cite our publication:

Jan Schroeder, Arthur Hsu, Samantha E. Boyle, Geoff MacIntyre, Marek Cmero, Richard W. Tothill, Ricky W. Johnstone, Mark Shackleton, and Anthony T. Papenfuss,
Socrates: Identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads,
Bioinformatics 2014 (Advance access) doi:10.1093/bioinformatics/btt767

Licensing

Socrates makes use of external libraries that are licensed under Apache License Version 2.0 and The MIT License. The GNU General Public License Version 3 (GPLv3) applies to the Socrates programs itself. By downloading or using this program you are also agreeing to these licenses.