FEATnotator 1.1.2 – Annotation of Sequence Features and Variation, Facilitating Interpretation in Genomics Experiments

FEATnotator 1.1.2

:: DESCRIPTION

FEATnotator is a light weight, fast and easy to use, open source software program that annotates different kinds of next generation analysis data based on known reference genome annotation information.

::DEVELOPER

FEATnotator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • R

:: DOWNLOAD

 FEATnotator

:: MORE INFORMATION

Citation:

FEATnotator: A Tool for Integrated Annotation of Sequence Features and Variation, Facilitating Interpretation in Genomics Experiments.
Podicheti R, Mockaitis K.
Methods. 2015 Apr 28. pii: S1046-2023(15)00175-9. doi: 10.1016/j.ymeth.2015.04.028

RUbioSeq 3.7 – Parallelized pipelines to automate Exome Variation and Bisulfite-seq Analyses

RUbioSeq 3.7

:: DESCRIPTION

RUbioSeq has been developed to facilitate the primary and secondary analysis of resequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically.

::DEVELOPER

Miriam Rubio-Camarillo at Spanish National Cancer Research Centre (CNIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java
  • Samtools
  • Fastqc

:: DOWNLOAD

 RUbioSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1687-9. doi: 10.1093/bioinformatics/btt203. Epub 2013 Apr 28.
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.
Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG.

eigenR2 1.0 – Dissecting Variation in High-dimensional studies

eigenR2 1.0

:: DESCRIPTION

eigen-R(2) is a new statistical algorithm and software package for dissecting the variation of a high-dimensional biological dataset with respect to other measured variables of interest.

::DEVELOPER

STOREY LAB | Princeton University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 eigenR2

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Oct 1;24(19):2260-2. doi: 10.1093/bioinformatics/btn411. Epub 2008 Aug 20.
Eigen-R2 for dissecting variation in high-dimensional studies.
Chen LS1, Storey JD.

fCNV – Detecting Copy Number Variation in a Fetal Genome

fCNV

:: DESCRIPTION

fCNV is a probabilistic method for non-invasive analysis of de novo CNVs in fetal genome based on maternal plasma sequencing

::DEVELOPER

Computational Biology Lab at the University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Python

:: DOWNLOAD

 fCNV

:: MORE INFORMATION

Citation:

Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing.
Rampášek L, Arbabi A, Brudno M.
Bioinformatics. 2014 Jun 15;30(12):i212-i218. doi: 10.1093/bioinformatics/btu292.

PICMI – Map Nucleotide and Amino Acid Variations on Genomes

PICMI

:: DESCRIPTION

The PICMI  (Perhaps I Can Map It)  server is an easy to use tool for quickly mapping one or more amino acid or nucleotide variations on a genome and its products, including alternatively spliced isoforms.

::DEVELOPER

the Biocomputing Unit

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PICMI: mapping point mutations on genomes.
Le Pera L, Marcatili P, Tramontano A.
Bioinformatics. 2010 Nov 15;26(22):2904-5. doi: 10.1093/bioinformatics/btq547. Epub 2010 Oct 12.

VarDetect – Sequence Variation Exploration tool

VarDetect

:: DESCRIPTION

VarDetect is a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces.

::DEVELOPER

Genome Institute, BIOTEC

:: SCREENSHOTS

VarDetect

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • Java

:: DOWNLOAD

 VarDetect

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S9. doi: 10.1186/1471-2105-9-S12-S9.
VarDetect: a nucleotide sequence variation exploratory tool.
Ngamphiw C, Kulawonganunchai S, Assawamakin A, Jenwitheesuk E, Tongsima S.

CNVineta 1.0-1 – Data mining tool for large case-control copy number variation data sets

CNVineta 1.0-1

:: DESCRIPTION

CNVineta is a flexible data mining tool for the analysis of copy number variations (CNVs) in large case-control SNP array data sets. The tool is available as an R statistical package. CNVineta offers a flexible and fast access to CNVs by a quick graphical overview in large case-control datasets. In addition, CNVineta provides rapid access to the log2 of raw data ratios (LRR) and B-allele frequencies (BAF) of specific or all samples, thereby allowing for a fast verification of the underlying raw data. CNVineta is also equipped with analysis methods for genome-wide screening for associated rare as well as common CNVs. Hence, CNVineta is a unique data mining tool to rapidly explore CNVs in large case-control data sets.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 CNVineta

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2208-9. Epub 2010 Jul 6.
CNVineta: a data mining tool for large case-control copy number variation datasets.
Wittig M, Helbig I, Schreiber S, Franke A.

FishingCNV 2.1 – Detecting rare Copy Number Variations in Exome-sequencing data

FishingCNV 2.1

:: DESCRIPTION

FishingCNV is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs.

::DEVELOPER

Yuhao Shi (yuhao.shi@mail.mcgill.ca)

:: SCREENSHOTS

FishingCNV

:: REQUIREMENTS

  • Linux /MacOsX/ Windows
  • R package
  • Java 

:: DOWNLOAD

 FishingCNV

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1461-2. doi: 10.1093/bioinformatics/btt151. Epub 2013 Mar 28.
FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data.
Shi Y1, Majewski J.

DELISHUS – Computing Genomic Deletion Variation

DELISHUS

:: DESCRIPTION

DELISHUS is an algorithm for detecting deletions in shared haplotypes using SNPs.It is an algorithmic framework for finding inherited and de novo deletions in a GWAS SNP dataset consisting of trios or pairs

::DEVELOPER

The Istrail Laboratory of Brown University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

  DELISHUS

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 15;28(12):i154-62. doi: 10.1093/bioinformatics/bts234.
DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism.
Aguiar D, Halldórsson BV, Morrow EM, Istrail S.

Genevar 3.3.0 – GENe Expression VARiation

Genevar 3.3.0

:: DESCRIPTION

Genevar is a database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression in eQTL studies.

::DEVELOPER

Professor Emmanouil Dermitzakis

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Genevar , source code

:: MORE INFORMATION

Citation

Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.
Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P and Dermitzakis ET
Bioinformatics (Oxford, England)2010;26;19;2474-6