SVDetect 0.8b – Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data

SVDetect 0.8b

:: DESCRIPTION

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SVDetect

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1895-6.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

Seqpare v1.0.0 – Novel Metric of Similarity between Genomic Interval Sets

Seqpare v1.0.0

:: DESCRIPTION

Seqpare is a self-consistent metric and tool for comparing sequences based on the total effective overlaps of their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, which directly represents the percentage of their effective overlapping: a similarity index of zero indicates totally unrelated sequences, and an index of one means that the interval sets are exactly the same.

::DEVELOPER

Seqpare team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Seqpare

:: MORE INFORMATION

Citation

Feng SC, Sheffield NC, Feng J.
Seqpare: a novel metric of similarity between genomic interval sets.
F1000Res. 2020 Jun 9;9:581. doi: 10.12688/f1000research.23390.2. PMID: 33500773; PMCID: PMC7808057.

LOLA 1.24.0 / LOLAweb – Genomic Locus Overlap Enrichment Analysis

LOLA 1.24.0 / LOLAweb

:: DESCRIPTION

LOLA (Locus Overlap Analysis) is an R Bioconductor package for genomic locus overlap enrichment. LOLA lets you test your genomic ranges of interest against a database of other genomic range sets to identify enrichment of overlap, tying external annotation to your regions of interest.

LOLAweb is server with public hosting of our shiny interface to the LOLA R-package.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 LOLA

:: MORE INFORMATION

Citation

Nagraj VP, Magee NE, Sheffield NC.
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis.
Nucleic Acids Res. 2018 Jul 2;46(W1):W194-W199. doi: 10.1093/nar/gky464. PMID: 29878235; PMCID: PMC6030814.

LOLA: Enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
Sheffield NC, Bock C.
Bioinformatics. 2015 Oct 27. pii: btv612.

trioPhaser – Using Mendelian inheritance logic to improve Genomic Phasing of Trios

trioPhaser

:: DESCRIPTION

trioPhaser is a containerized software tool that uses both Mendelian inheritance logic and SHAPEIT4 to phase trios when gVCF files are available.

::DEVELOPER

trioPhaser team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Docker
  • Python

:: DOWNLOAD

trioPhaser

:: MORE INFORMATION

Citation

Miller DB, Piccolo SR.
trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios.
BMC Bioinformatics. 2021 Nov 22;22(1):559. doi: 10.1186/s12859-021-04470-4. PMID: 34809557; PMCID: PMC8607709.

GSA v1.0 – Genomic Scar Analysis

GSA v1.0

:: DESCRIPTION

The GSA method is an independent development algorithm for calling copy number and detecting Homologous Recombination Deficiency (HRD) from target capture sequencing.

::DEVELOPER

GSA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

GSA

:: MORE INFORMATION

Citation

Chen D, Shao M, Meng P, Wang C, Li Q, Cai Y, Song C, Wang X, Shi T.
GSA: an independent development algorithm for calling copy number and detecting homologous recombination deficiency (HRD) from target capture sequencing.
BMC Bioinformatics. 2021 Nov 23;22(1):562. doi: 10.1186/s12859-021-04487-9. PMID: 34814825; PMCID: PMC8609767.

GoMiner Build454- Resource for Biological Interpretation of Genomic and Proteomic data

GoMiner Build454

:: DESCRIPTION

GoMiner organizes and allows the visualization of large sets of genes based on Gene Ontology classifications.GoMiner is a tool for biological interpretation of ‘omic’ data – including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question

::DEVELOPER

GoMiner Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

 GoMiner

:: MORE INFORMATION

Citation:

Barry R Zeeberg et al.
GoMiner: a resource for biological interpretation of genomic and proteomic data
Genome Biology 2003, 4:R28

ClineHelpR v1.1 – Genomic Cline Outlier Detection and Visualization

ClineHelpR v1.1

:: DESCRIPTION

ClineHelpR is an R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, bgc and Introgress

::DEVELOPER

Bradley Martin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R

:: DOWNLOAD

ClineHelpR

:: MORE INFORMATION

Citation

Martin BT, Chafin TK, Douglas MR, Douglas ME.
ClineHelpR: an R package for genomic cline outlier detection and visualization.
BMC Bioinformatics. 2021 Oct 16;22(1):501. doi: 10.1186/s12859-021-04423-x. PMID: 34656096; PMCID: PMC8520269.

libCSAM – Lossy Compression of Quality Scores in Genomic data

libCSAM

:: DESCRIPTION

libCSAM will contain several C++ codes for compress,decompress, and access each of the fields of any SAM format file.

::DEVELOPER

Rodrigo Cánovas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 libCSAM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 2.
Lossy compression of quality scores in genomic data.
Cánovas R1, Moffat A, Turpin A.

SVS 8 – Analytic Tools for Genomic and Phenotypic data

SVS 8

:: DESCRIPTION

SVS (SNP & Variation Suite) is an integrated collection of user-friendly, yet powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data. SVS was created specifically to empower biologists and other researchers to easily perform complex analyses and visualizations, eliminating the need to rely exclusively on bioinformatics experts or cobble together difficult to use, incompatible freeware. With SVS you can focus on your research instead of learning to be a programmer or waiting in line for bioinformaticians.

::DEVELOPER

Golden Helix

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 SVS

:: MORE INFORMATION

GGV / PlasmoView – The Global Genomic Visualiser

GGV / PlasmoView

:: DESCRIPTION

GGV is a webtool designed to share large genomic datasets with important stakeholders, including research partners, policy makers, clinicians and the public.

::DEVELOPER

Dr Mark Preston

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GGV

:: MORE INFORMATION

Citation

MD Preston and TG Clark:
GGV: An open resource for visualising global genomic variation,
submitted.

PlasmoView: A web-based resource to visualise global malaria genomic variation.
M.D. Preston, S.A. Assefa, H. Ocholla, C.J Sutherland, S. Borrmann, A. Nzila, P. Michon, TT Hien, T Bousema, C.J. Drakeley, I. Zongo, J.B. Ouedraogo, A.A. Djimde, O.K. Doumbo, F. Nosten, R.M. Fairhurst, D.J. Conway, C. Roper and T.G. Clark
J Infect Dis. 2014 Jun 1;209(11):1808-15. doi: 10.1093/infdis/jit812.

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