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SVMerge specifications

Information


Unique identifier OMICS_00325
Name SVMerge
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SVMerge

SVMerge citations

 (7)
library_books

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low Coverage Genomes

2017
Genome Biol Evol
PMCID: 5737362
PMID: 28985298
DOI: 10.1093/gbe/evx170

[…] accessed September 2017. Easy configuration and the modular architecture make it convenient to adapt TeddyPi to process data from a broad range of TE/SV callers or other integration pipelines such as SVMerge or McClintock (; ). TeddyPi can be applied to any group of organisms where accurate TE/SV calling is feasible. […]

call_split

Genome characterization of the selected long and short sleep mouse lines

2016
Mamm Genome
PMCID: 5110614
PMID: 27651241
DOI: 10.1007/s00335-016-9663-6
call_split See protocol

[…] ncorporating the most high-confidence set of SNPs and small indels for each strain into the mm10 reference (common and strain-distinct).Large structural variations (SVs; >50 bp) were called using the SVMerge pipeline (v1.2r37; Wong et al. ) which integrates results from multiple SV callers: BreakDancerMax (v1.1.2; Chen et al. ) was run independently on each DNA sequencing library (10 kb, 4 kb, 300 […]

library_books

Discovery and characterization of Alu repeat sequences via precise local read assembly

2015
Nucleic Acids Res
PMCID: 4666360
PMID: 26503250
DOI: 10.1093/nar/gkv1089

[…] next-generation sequencing data for breakpoint identification. Tools such as TIGRA (), a modification of the SGA assembler used in HYDRA-MULTI (,), and the use of a de brujin graph-based approach in SVMerge () have been developed to assemble structural variant breakpoints from population scale or heterogeneous tumour sequencing studies. Assembly-based approaches have also lead to increased sensit […]

library_books

Identification of large scale genomic variation in cancer genomes using in silico reference models

2015
Nucleic Acids Res
PMCID: 4705683
PMID: 26264669
DOI: 10.1093/nar/gkv828

[…] ome or the CIGAR value has significant numbers of soft-clipped bases (e.g. partially aligned reads). As these methods often limit the size of the variants they can detect consensus approaches such as SVMerge () are often used to increase detection across all types.While the reference based approach is widely used, it suffers from a number of limitations inherent to current alignment algorithms, an […]

library_books

Copy number variation analysis in the context of electronic medical records and large scale genomics consortium efforts

2014
Front Genet
PMCID: 3957100
PMID: 24672537
DOI: 10.3389/fgene.2014.00051

[…] r review), and the most effective strategy in terms of minimizing erroneous CNV calls is to incorporate multiple toolsets, which can be validated computationally via local de novo assembly (e.g., see SVMerge, ). […]

library_books

A survey of tools for variant analysis of next generation genome sequencing data

2013
Brief Bioinform
PMCID: 3956068
PMID: 23341494
DOI: 10.1093/bib/bbs086

[…] ch were automatically reduced to 2529 and 207, respectively. Although GASVPro commands offer to call inter-chromosomal variations, the feature is not yet supported by its pipeline scripts. Testing of SVMerge was aborted, as installation dependencies are likely beyond the IT skill levels of many bench scientists.In summary, all selected tools for variant identification were successfully installed a […]

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SVMerge institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

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