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GASVPro specifications

Information


Unique identifier OMICS_00317
Name GASVPro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A or some aligned read(s)
Input format SAM,BAM
Biological technology Illumina
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.4
Stability Stable
Source code URL https://code.google.com/archive/p/gasv/
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Benjamin Raphael <>
  • person_outline Suzanne Sindi <>

Publication for GASVPro

GASVPro in pipeline

2015
PMCID: 4647614
PMID: 26572918
DOI: 10.1186/s12864-015-2154-4

[…] nucleotide polymorphisms (snps) with seqmanngen11(dnastar) tool using 90 % of the snp carrying reads as the cutoff parameter for selection. the structural variation analysis was performed with gasvpro []., metabolite analysis was performed using the accella1250™ hplc system coupled with the benchtop es-ms orbitrap exactive™ (thermo fisher scientific, san jose, ca). a sample of 5 μl […]


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GASVPro in publications

 (6)
PMCID: 5826927
PMID: 29483503
DOI: 10.1038/s41467-018-03273-1

[…] and dissect, which are rna-seq analysis tools that can also be used to analyze genomic data). there are also several tools that employ a combination of these (e.g., pindel, delly, novobreak, and gasvpro), which, unfortunately, only consider uniquely mapped reads and cannot identify alterations in repetitive dna. in fact, no available tool, even those designed to identify gene fusions […]

PMCID: 5679599
PMID: 29121641
DOI: 10.1371/journal.pone.0187617

[…] were kept for further analysis. we used three different software to identify structural variants (sv) from this mate-pair sequencing data: delly (doi: 10.1093/bioinformatics/bts378), svdetect [] and gasvpro []. all three software were used with default parameters. only translocations that were supported by more than 10 mate-pairs were considered as reliable candidate translocations. […]

PMCID: 4647614
PMID: 26572918
DOI: 10.1186/s12864-015-2154-4

[…] assemblies of nrrl1951, ds17690 and ds68530 strain. to simplify the following comparative analysis these snps were subtracted from the mutational profiles of the subjected strains. an analysis using gasvpro [] did not reveal any structural variation between the strains., in order to assess the distribution of snps across genes involved in different cellular processes, we performed a functional […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] rc for the detection of large events and rp for accurate identification of breakpoints can reduce the number of false positive calls [svdetect (zeitouni et al., ), cnver (medvedev et al., ), gasvpro (sindi et al., ), and ingap-sv (qi and zhao, )]. genome strip (handsaker et al., ) exploits rp, rc, sr, and population-scale patterns to detect genome structural polymorphisms., packages […]

PMCID: 3634047
PMID: 23637806
DOI: 10.1371/journal.pone.0061292

[…] sv-detection algorithms will keep evolving to implement sound statistical models with estimates of both false positives and false negatives., one step in this direction is the recent appearance of gasvpro, an sv-detection algorithm that implements a probabilistic model to determine the most likely set of structural variants supported by pem data from one individual . gasvpro uses multiple […]


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GASVPro institution(s)
Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Department for Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA; Department of Computer Science, Brown University, Providence, RI, USA
GASVPro funding source(s)
Supported by National Institutes of Health (R01 HG5690) and Burroughs Wellcome Career Award at the Scientific Interface.

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