HTML C++ C Makefile Assembly Ada Other
Latest commit 83a7ebb Feb 26, 2017 fritzsedlazeck bug fix in calc position
Failed to load latest commit information.
lib Major release of Sniffles: Oct 14, 2016
src bug fix in calc position Feb 27, 2017
CMakeLists.txt Bug fix for picardtools, calling large insertions Jan 18, 2017
LICENSE Initial commit Oct 25, 2015 Reformatting Dec 27, 2016


Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled! If you experience problems or have suggestions please contact:

Please see our github wiki for more information (

NextGenMap-LR: (NGM-LR)

Sniffles performs best with the mappings of NGM-LR our novel long read mapping method. Please see:

Poster & Talks:

Accurate and fast detection of complex and nested structural variations using long read technologies Biological Data Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 26 - 29.10.2016

NextGenMap-LR: Highly accurate read mapping of third generation sequencing reads for improved structural variation analysis Genome Informatics 2016, Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK, 19.09.-2.09.2016