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README.md

Sniffles

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: fritz.sedlazeck@gmail.com

Please see our github wiki for more information (https://github.com/fritzsedlazeck/Sniffles/wiki)


NextGenMap-LR: (NGM-LR)

Sniffles performs best with the mappings of NGM-LR our novel long read mapping method. Please see: https://github.com/philres/nextgenmap-lr


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