Tag: Whole-exome Sequencing

TREVA 1 – Bioinformatics Pipelines for Targeted Resequencing and Whole-exome Sequencing

TREVA

:: DESCRIPTION

TREVA (Targeted REsequencing Virtual Appliance) is a user-friendly virtual appliance, containing complex bioinformatics pipelines that can be installed and setup with minimal efforts. TREVA pipelines support a series of analyses commonly required for targeted resequencing and whole exome sequencing data, including: single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses.

::DEVELOPER

TREVA team

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

:: DOWNLOAD

 TREVA

:: MORE INFORMATION

Citation:

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.
Li J, Doyle MA, Saeed I, Wong SQ, Mar V, Goode DL, Caramia F, Doig K, Ryland GL, Thompson ER, Hunter SM, Halgamuge SK, Ellul J, Dobrovic A, Campbell IG, Papenfuss AT, McArthur GA, Tothill RW.
PLoS One. 2014 Apr 21;9(4):e95217. doi: 10.1371/journal.pone.0095217.

EXCAVATOR 2.2 / EXCAVATOR2 1.1.2 / XCAVATOR – Tool for Detecting CNVs from Whole-exome Sequencing data

EXCAVATOR 2.2 / EXCAVATOR2 1.1.2 / XCAVATOR

:: DESCRIPTION

EXCAVATOR is a novel software package for the detection and classification of genomic regions involved in copy numner variants that uses whole-exome sequencing data generated by second generation sequencing technologies.

EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads.

XCAVATOR is a novel software package for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments.

::DEVELOPER

EXCAVATOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux
  • R package
  • Perl
  • Fortron

:: DOWNLOAD

 EXCAVATOR / EXCAVATOR2 / XCAVATOR

:: MORE INFORMATION

Citation

Magi A, Pippucci T, Sidore C.
XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.
BMC Genomics. 2017 Sep 21;18(1):747. doi: 10.1186/s12864-017-4137-0. PMID: 28934930; PMCID: PMC5609061.

D’Aurizio R, Pippucci T, Tattini L, Giusti B, Pellegrini M, Magi A.
Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2.
Nucleic Acids Res. 2016 Nov 16;44(20):e154. doi: 10.1093/nar/gkw695. Epub 2016 Aug 9. PMID: 27507884; PMCID: PMC5175347.

Genome Biol. 2013;14(10):R120.
EXCAVATOR: detecting copy number variants from whole-exome sequencing data.
Magi A, Tattini L, Cifola I, D’Aurizio R, Benelli M, Mangano E, Battaglia C, Bonora E, Kurg A, Seri M, Magini P, Giusti B, Romeo G, Pippucci T, De Bellis G, Abbate R, Gensini GF.

H3M2 20131219 – Detection of ROH from Whole-exome Sequencing data

H3M2 20131219

:: DESCRIPTION

H3M2 is novel computational approach for the identification of Runs of Homozygosity by using whole-exome sequencig data generated by second generation sequencig technologies

::DEVELOPER

H3M2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 H3M2

:: MORE INFORMATION

Citation

H3M2: Detection of Runs of Homozygosity from whole-exome sequencing data.
Magi A, Tattini L, Palombo F, Benelli M, Gialluisi A, Giusti B, Abbate R, Seri M, Gensini GF, Romeo G, Pippucci T.
Bioinformatics. 2014 Jun 24. pii: btu401.

DeAnnCNV – Detection and Annotation of Copy Number Variations from Whole-exome Sequencing data

DeAnnCNV

:: DESCRIPTION

DeAnnCNV, an online tool, designed for precise Detection and Annotation of Copy Number Variations (CNVs) from whole-exome sequencing (WES) data.

::DEVELOPER

BioStaCs group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data.
Zhang Y, Yu Z, Ban R, Zhang H, Iqbal F, Zhao A, Li A, Shi Q.
Nucleic Acids Res. 2015 May 26. pii: gkv556.

ClinLabGeneticist 2.28 – Diagnosis of Pathogenic Variants from WES data

ClinLabGeneticist 2.28

:: DESCRIPTION

ClinLabGeneticist is a tool to assist geneticist for diagnosis of pathogenic variants from WES ( whole exome sequencing) data.

::DEVELOPER

Rong Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ClinLabGeneticist

:: MORE INFORMATION

Citation

ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories.
Wang J, Liao J, Zhang J, Cheng WY, Hakenberg J, Ma M, Webb BD, Ramasamudram-Chakravarthi R, Karger L, Mehta L, Kornreich R, Diaz GA, Li S, Edelmann L, Chen R.
Genome Med. 2015 Jul 29;7(1):77. doi: 10.1186/s13073-015-0207-6.

Exomiser 12.1.0 – Annotates Variants from Whole-exome Sequencing Data

Exomiser 12.1.0

:: DESCRIPTION

The Exomiser is a Java program that functionally annotates and prioritises variants from whole-exome sequencing data starting from a VCF file.

::DEVELOPER

The Computational Biology @ Charité Berlin at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 Exomiser

:: MORE INFORMATION

Citation

Improved exome prioritization of disease genes through cross-species phenotype comparison.
Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D.
Genome Res. 2014 Feb;24(2):340-8. doi: 10.1101/gr.160325.113.

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