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 NGM-LR with the optional SAM attributes enabled! If you experience problems or have suggestions please contact: [email protected]

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

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

Please see and cite our preprint: http://www.biorxiv.org/content/early/2017/07/28/169557

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

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

Arabidopsis trio:

• http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/Arabidopsis_trio .

Genome in the Bottle trio:

• Mappings: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/Baylor_NGMLR_bam_GRCh37/ .

• SV calls: http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/GiaB/

NA12878:

• http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/NA12878/ .

SKBR3:

• http://labshare.cshl.edu/shares/schatzlab/www-data/fsedlaze/Sniffles/Skbr3/ .