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sniffles's Introduction

Sniffles

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)


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


Citation:

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


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


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:

NA12878:

SKBR3:

sniffles's People

Contributors

fritzsedlazeck avatar lh3 avatar 0xaf1f avatar

Watchers

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