Software and Tools to detect structure variation with long reads !!
Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs detectable by short-read data.
With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:
- Uncover missing heritability linked to structural variation
- Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
- Resolve structural variation across the complete size spectrum with basepair resolution
Following are the SV tools, which can assist you to achieve your goal.
Sniffles: Structural variation caller using third generation sequencing
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!
More at https://github.com/fritzsedlazeck/Sniffles
MultiBreak-SV: It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.
More at https://github.com/raphael-group/multibreak-sv
Parliament: A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?
Publication about the algorithm and “…the first long-read characterization of structural variation in a diploid human personal genome…” (HS1011) - “Assessing structural variation in a personal genome—towards a human reference diploid genome”
More at https://sourceforge.net/projects/parliamentsv/
https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf
PBHoney: the structural variation discovery tool
PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.
Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract
More at https://sourceforge.net/projects/pb-jelly/
SMRT-SV: Structural variant and indel caller for PacBio reads
Structural variant (SV) and indel caller for PacBio reads based on methods from Chaisson et al. 2014.
SMRT-SV provides an official software package for tools described in Chaisson et al. 2014 and adds several key features including the following.
- Unified variant calling user interface with built-in cluster compute support
- Small indel calling (2-49 bp)
- Improved inversion calling (
screenInversions) - Quality metric for SV calls based on number of local assemblies supporting each call
- Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions
- Genotyping of SVs with Illumina paired-end reads from WGS samples
