MICC 1.0 – Model based Interaction Calling from ChIA-PET data

MICC 1.0

:: DESCRIPTION

MICC is an R package which provides methods to detect chromatin interactions from ChIA-PET data.

::DEVELOPER

MICC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

 MICC

:: MORE INFORMATION

Citation

MICC: an R package for identifying chromatin interactions from ChIA-PET data.
He C, Zhang MQ, Wang X.
Bioinformatics. 2015 Jul 31. pii: btv445.

SpliceJumper – Splicing Junction Calling from RNA-Seq data

SpliceJumper

:: DESCRIPTION

SpliceJumper is a classification based approach for calling splicing junctions from RNA-seq data

::DEVELOPER

Simon C Chu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SpliceJumper

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015;16 Suppl 17:S10. doi: 10.1186/1471-2105-16-S17-S10. Epub 2015 Dec 7.
SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data.
Chu C, Li X, Wu Y.

CHIAMANTE 1.0.3 – Joint Genotype Calling algorithm for Array and Sequence data

CHIAMANTE 1.0.3

:: DESCRIPTION

Chiamante is a genotype caller for Illumina Beadchips that can augment microarray data with genotype likelihoods from sequence data for improved genotype accuracy and call rate. Whilst primarily designed to call genotypes via fusing these two sources of information, Chiamante also functions as a highly accurate array-only caller.

::DEVELOPER

Jared O’Connell and Jonathan Marchini.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CHIAMANTE

:: MORE INFORMATION

Citation

J O’Connell, J. Marchini (2012)
Joint Genotype Calling With Array and Sequence Data.
Genetic Epidemiology. 10.1002/gepi.21657

FermiKit 0.13 – De novo Assembly based Variant Calling pipeline for Illumina Short Reads

FermiKit 0.13

:: DESCRIPTION

FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FermiKit

:: MORE INFORMATION

Citation

FermiKit: assembly-based variant calling for Illumina resequencing data.
Li H.
Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440.

deepSNV 1.16.0 – Calling Subclonal SNVs from paired Deep Sequencing Experiments

deepSNV 1.16.0

:: DESCRIPTION

deepSNV is an R package for calling subclonal single-nucleotide variants from paired deep sequencing experiments.This package provides provides a quantitative variant caller for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. It assumes a comparative setup with a control experiment of the same loci and a beta-binomial model to discriminate sequencing errors and subclonal SNVs.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

deepSNV

:: MORE INFORMATION

Citation

Nat Commun. 2012 May 1;3:811. doi: 10.1038/ncomms1814.
Reliable detection of subclonal single-nucleotide variants in tumour cell populations.
Gerstung M1, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N.

CHIAMO 0.2.1 – Genotype Calling Algorithm for Multi-cohort Study

CHIAMO 0.2.1

:: DESCRIPTION

CHIAMO is a program for calling genotypes from the Affymetrix 500K Mapping chip. The program allows for multiple cohorts which have potentially different intensity characteristics that can lead to elevated false-positive rates in genome-wide studies. The underlying model has a hierarchical structure that allows for correlation between the parameters of each cohort.

::DEVELOPER

Chris Spencer,  Jonathan Marchini, Peter Donnelly, YY Teo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  CHIAMO

:: MORE INFORMATION

Citation

J. Marchini, B. Howie, S. Myers, G. McVean and P. Donnelly (2007)
A new multipoint method for genome-wide association studies via imputation of genotypes.
Nature Genetics 39 : 906-913