Address of the bookmark: http://4dgenome.research.chop.edu/

Structural variants (SVs) such as deletions, insertions, duplications, inversions and translocations litter genomes and are often associated with gene expression changes and severe phenotypes (ie. genetic diseases in humans). Recent studies on the functional aspects of different types of SVs have unveiled several cases of adaptive evolution. For example, inversions have been associated with ecological adaptations and may facilitate speciation. Due to their prevalent nature, SVs arguably have a large impact on genome evolution and should not be neglected when studying the genetics of adaptation and speciation. SVs were classically defined as chromosomal rearrangements larger than 1kb, but due to a higher resolution of new detection methods, smaller variants (between 50 and 1000 base pairs) can now be accurately assessed. Besides various methods of detection in next generation sequencing data (paired end mapping, split reads, and depth of coverage), array-based approaches have proven to be particularly useful for detecting copy number variations (CNVs). These technologies have enabled researchers to catalog a wide spectrum of SVs in many organisms and infer the effects of selection shaping their evolutionary trajectories.

Structure variation sequencing signature (Source: NatRev Genetics)

Related tools, databases and publications are listed below. If you know any interesing papers, please let us know in comment section:

Key concepts

Structural variation includes balanced variants such as inversions and translocations, and unbalanced ones such as duplications and deletions (copy number variations or CNVs).

Structural variants can arise by several mechanisms, including nonallelic homologous recombination (NAHR), nonhomologous end‐joining (NHEJ) and DNA replication‐based fork stalling and template switching (FoSTeS).

CNV is closely linked to segmental duplication, but is not exactly the same. Segmental duplications can stimulate CNV formation by NAHR, and themselves arise from CNVs that have become fixed.

Segmental duplications did not appear uniformly during the evolution of the Great Ape species, but rather during a burst of activity around the time of the divergence of gorilla from the human/chimpanzee ancestor.

Duplicated genes play a critical role in the evolution of a genome as they act as ‘spare parts’ than can evolve to perform new or more specialized functions.

Effects of structural variation on gene expression can be identified but only a few examples of the consequences for species biology have been documented.

Tools

CNVnatora tool for CNV discovery and genotyping from depth of read mapping.2011a,2011b

AGEa tools that implements an algorithm for optimal alignment of sequences with SVs.2011

BreakSeqa pipeline for annotation, classification and analysis of SVs at single nucleotide resolution.2010

PEMera computational and simulation framework for discovering SVs by paired-end read mapping.2009,2007

GASV https://code.google.com/archive/p/gasv/

PAIROSCOPE http://pairoscope.sourceforge.net/

SVDetect http://svdetect.sourceforge.net/Site/Home.html

BreakPtr, discovery of unbalanced structural variants (copy-number variants) with tiling microarrays Link 

R Package https://www.bioconductor.org/help/course-materials/2010/EMBL2010/Practical-4-StructuralVariants.pdf

BreakSeq, structural variant genotyping using split reads Link 

CopySeq, genotyping of unbalanced structural variants (copy-number variants) using read-depth Link 

DELLY2, integrated structural variant discovery, genotyping and visualization in deep sequencing data Link 

PEMer, structural variant discovery in 454 sequencing data by paired-end mapping Link 

TIGER, transduction inference in germline genomes using short read data Link 

MANTA https://github.com/Illumina/manta

SV-Bay https://github.com/InstitutCurie/SV-Bay

BreakDancer http://breakdancer.sourceforge.net/

Variation Hunter http://compbio.cs.sfu.ca/software-variation-hunter

Lumpy https://github.com/arq5x/lumpy-sv

ForestSV http://sebatlab.ucsd.edu/index.php/software-data 

PBSuites for long reads https://sourceforge.net/projects/pb-jelly/

Visualization

The SV visualization tool: http://genomesavant.com/savant/

InGAP-SV (http://ingap.sourceforge.net/) that is nice tools for both detection and visualisation of severals kind of structural variations (Large insertions, translocation, deletion, inversions....) 

Tools table: http://www.nature.com/nbt/journal/v29/n8/fig_tab/nbt.1904_T2.html

Variation Viewer https://www.ncbi.nlm.nih.gov/variation/view/

Papers

http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1858.html

http://journal.frontiersin.org/researchtopic/1412/structural-variations-in-genomes-ecological-and-evolutionary-implications

http://www.mi.fu-berlin.de/wiki/pub/ABI/GenomicsLecture10Materials/structural-variation.pdf

http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1479-3

https://www.ncbi.nlm.nih.gov/dbvar/content/overview/

http://www.nature.com/subjects/structural-variation

https://eichlerlab.gs.washington.edu/news/NatMeth_Feb2012.pdf

https://www.ncbi.nlm.nih.gov/pubmed/19477992 ***

https://www.ncbi.nlm.nih.gov/pubmed/22452995

http://biorxiv.org/content/early/2016/09/06/073833

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479793/

http://www.nature.com/articles/srep18501

http://www.genetics.org/content/202/1/351

http://www.cs.cmu.edu/~sssykim/teaching/s13/slides/Lecture_SVI.pdf

https://www.omicsonline.org/open-access/structural-variation-detection-from-next-generation-sequencing-2469-9853-S1-007.php?aid=69055

http://schatzlab.cshl.edu/presentations/2016/2016.01.12.PAG.Structural%20Variations.pdf

Basic usage:

Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf
-or-
Rscript Ideoplot.R --annotate annotations.bed

Options
  --ideobed, i      A bed file of reference contig lengths/chromosome names
  --heatmap, -h     Fill chromosomes with normalized heatmap
                   (described below)
  --annotate, -a    Add character annotations.
  --out, -o         PDF output name.
  --stripes, -s     Specify a file containing the layout of the
                    annotations (description below)
  --bars, -b        Add track annotations
  --reference, -f   Either hg19, or hg38
  --topdown, r      Flag, when set, flips the orientation (P arms
                    drawn on top).

Address of the bookmark: https://github.com/mchaisso/Ideoplot

Address of the bookmark: http://www.bcgsc.ca/platform/bioinfo/software/sockeye/releases/1.3

Know of any other open source software for PacBio data? Email us.

Software categories:

• De novo assembly
• Structural Variations Detection
• Reference-based alignment
• Consensus and variant calling
• RNA analysis
• Epigenetic base modifications and methylation
• Barcoding
• Genome Browsers
• Run QC
• Frameworks and APIs

Address of the bookmark: https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software

More at http://pandeylab.igm.jhmi.edu/

http://scholar.google.com/citations?user=OhuG0FcAAAAJ&hl=en

RNAs, especially non-coding RNAs (such as microRNA, long ncRNAs) are recently identified to be very abundant in mammalian organisms and play some key roles in gene expression regulation, gene silencing, and also implicated in disease progression, stem cell pluripotency etc. Current research activities of our lab include analysis of expression pattern of ncRNAs by microarray and next-gen sequencing data and understanding the role of miRNAs or other regulatory RNAs in various diseases, especially cancer and validation by reporter assays (renilla/luciferase) and other experimental tools.

More @ http://vvekslab.in/index.html

Research Interest
Genomic Data Integration

Microarray Analysis

Gene and Protein Function Prediction

Detection and Analysis of Chromosomal Abnormalities and Functional Evolution

Integration of Computation and Experiments

Identification of Biological Networks and Pathways

Evaluation and Validation of Computational Predictions

Scalable Visualization-Based Data Analysis

More @ http://reducio.princeton.edu/cm/
PI page @ http://reducio.princeton.edu/cm/ogt

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/