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

Windows / Linux / MacOS
Oracle VirtualBox

:: 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.

Disperse 1.0.3 – Design of Selector Assays for Targeted Resequencing Applications

Disperse 1.0.3

:: DESCRIPTION

The Disperse project aims to develop and distribute software and data for design of selector assays for exon resequencing applications. The software consists of Java and Perl code integrated into a pipeline that performs all tasks required to transform a list of gene names to a set of selector probes targetting all exonic regions of those genes

::DEVELOPER

Disperse Team

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows / Linux
Java
Perl
Blast

:: DOWNLOAD

Disperse

:: MORE INFORMATION

Citation

J. Stenberg, M. Zhang and H. Ji
Disperse–a software system for design of selector probes for exon resequencing applications
Bioinformatics (2009) 25(5): 666-667

cnvCapSeq 0.1.2 – Detecting & Genotyping CNV in Long-range Targeted Resequencing

cnvCapSeq 0.1.2

:: DESCRIPTION

cvnCapSeq is a set of Java-based command-line tools for detecting and genotyping copy number variation (CNV) in targeted resequencing experiments of large contiguous genomic regions.

::DEVELOPER

cnvCapSeq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
JRE

:: DOWNLOAD

cnvCapSeq

:: MORE INFORMATION

Citation

cnvCapSeq: detecting copy number variation in long-range targeted resequencing data.
Bellos E, Kumar V, Lin C, Maggi J, Phua ZY, Cheng CY, Cheung CM, Hibberd ML, Wong TY, Coin LJ, Davila S.
Nucleic Acids Res. 2014 Nov 10;42(20):e158. doi: 10.1093/nar/gku849.

Contra 2.0.8 – Copy Number Analysis for Targeted Resequencing

Contra 2.0.8

:: DESCRIPTION

CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

::DEVELOPER

Contra team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux / MacOsX /Windows
Python
R package
BEDTools
SAMtools

:: DOWNLOAD

Contra

:: MORE INFORMATION

Citation

Li, et al.
CONTRA: copy number analysis for targeted resequencing
Bioinformatics (2012) 28 (10): 1307-1313.

MIPgen 1.1 – Analysis and Design of Molecular Inversion Probes for Targeted Resequencing

MIPgen 1.1

:: DESCRIPTION

MIPgen is a fast, simple way to generate designs for MIP (Molecular Inversion Probes) assays targeting hundreds or thousands of genomic loci in parallel.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

MIPgen

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 26. pii: btu353. [Epub ahead of print]
MIPgen: Optimized Modeling and Design of Molecular Inversion Probes for Targeted Resequencing.
Boyle EA1, O’Roak BJ2, Martin BK3, Kumar A3, Shendure J