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Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) 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 NGMLR with the optional SAM attributes enabled! If you experience problems or have suggestions please contact:

Please see our github wiki for more information (

How to build Sniffles

wget -O Sniffles.tar.gz
tar xzvf Sniffles.tar.gz
cd Sniffles-master/
mkdir -p build/
cd build/
cmake ..

cd ../bin/sniffles*

Note Mac users often have to provide parameters to the cmake command:

cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 .. 


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


Please see and cite our paper:

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

NGMLR: 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

Datasets used in the mansucript:

We provide the NGMLR aligned reads and the Sniffles calls for the data sets used:

Arabidopsis trio:

Genome in the Bottle trio: