Sniffles is a SV caller for long reads. It is mainly designed for PacBio reads, but also works on Oxford Nanopore reads. SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations). Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication). Furthermore, Sniffles incorporates multiple auto tuning functions to determine data set depending parameter to reduce the overall risk of falsely infer SVs.

Newest release

Code (.zip)

Code (.tar.gz)

wget https://github.com/fritzsedlazeck/Sniffles/archive/master.tar.gz -O Sniffles.tar.gz
tar xzvf Sniffles.tar.gz
cd Sniffles/
mkdir -p build/
cd build/
cmake ..
make

cd ../bin/sniffles*
./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 ..