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

:: 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.

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.

CNVer 0.8.1 – method for Detecting Copy Number Variation

CNVer 0.8.1

:: DESCRIPTION

CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

CNVer

:: MORE INFORMATION

Citation

Genome Res. 2010 Nov;20(11):1613-22. doi: 10.1101/gr.106344.110. Epub 2010 Aug 30.
Detecting copy number variation with mated short reads.
Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M.

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.

CanProVar 2.0 – Human Cancer Proteome Variation Database

CanProVar 2.0

:: DESCRIPTION

CanProVar is designed to store and display single amino acid alterations including both germline and somatic variations in the human proteome, especially those related to the genesis or development of human cancer based on the published literatures.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation.
Zhang M, Wang B, Xu J, Wang X, Xie L, Zhang B, Li Y, Li J.
J Proteome Res. 2017 Feb 3;16(2):421-432. doi: 10.1021/acs.jproteome.6b00505.

CNVphaser / CNVphaserPro 1.1 – Infer CNV Haplotypes with Variations

CNVphaser / CNVphaserPro 1.1

:: DESCRIPTION

CNVphaser infers haplotypes with variations in both copy numbers and nucleotide sequences within a CNV region

CNVphaserPro, a successor of CNVphaser and MOCSphaser to handle noisy CNV data such as microarray data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Perl

:: DOWNLOAD

CNVphaser / CNVphaserPro

:: MORE INFORMATION

Citation

Am J Hum Genet. 2008 Aug;83(2):157-69. doi: 10.1016/j.ajhg.2008.06.021. Epub 2008 Jul 17.
An algorithm for inferring complex haplotypes in a region of copy-number variation.
Kato M1, Nakamura Y, Tsunoda T.

findGSE – Estimating Genome Size Variation using k-mer Frequencies

findGSE

:: DESCRIPTION

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.

::DEVELOPER

KS’ Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R Package

:: DOWNLOAD

findGSE

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Feb 15;34(4):550-557. doi: 10.1093/bioinformatics/btx637.
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies.
Sun H, Ding J, Piednoël M, Schneeberger K.

WhopGenome 0.9.7 – High-speed Access to Whole-genome Variation Data

WhopGenome 0.9.7

:: DESCRIPTION

WhopGenome is a package for R that provides high-speed access to Variant Call Format (VCF) files as e.g. published by the 1000 Genomes Project.. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.

::DEVELOPER

Computational Cell Biology, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows / MacOsX
R

:: DOWNLOAD

WhopGenome

:: MORE INFORMATION

Citation

WhopGenome: high-speed access to whole genome variation and sequence data in R.
Wittelsbürger U, Pfeifer B, Lercher MJ.
Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636

RNAv – Search Genomes for RNA Secondary Structure Variation

RNAv

:: DESCRIPTION

RNAv (RNA secondary structure variation) is a program that searches for RNA secondary structure variations based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
C++ Complier

:: DOWNLOAD

RNAv

:: MORE INFORMATION

Citation

Huang, Z., Malmberg, R., Mohebbi M., and Cai, L. (2010)
RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism
Proceedings of Computational Systems Bioinformatics Conference (CSB 2010), August, 2010. Vol. 9, p. 56-69.