RepeatSeq v0.8.2 – Genotyping Microsatellite Repeats Tool

RepeatSeq v0.8.2

:: DESCRIPTION

RepeatSeq determines genotypes for microsatellite repeats in high-throughput sequencing data.

:: DEVELOPER

Mittelman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows
Python

:: DOWNLOAD

RepeatSeq

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jan 7;41(1):e32. doi: 10.1093/nar/gks981. Epub 2012 Oct 22.
Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.
Highnam G1, Franck C, Martin A, Stephens C, Puthige A, Mittelman D.

AffyPipe – Pipeline for Affymetrix Axiom Genotyping Workflow

AffyPipe

:: DESCRIPTION

AffyPipe allows you to edit SNP probe classes directly while exporting genotypes in PLINK format

::DEVELOPER

AffyPipe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsX / Linux
Python

:: DOWNLOAD

AffyPipe

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Nov 1;30(21):3118-9. doi: 10.1093/bioinformatics/btu486.
AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.
Nicolazzi EL, Iamartino D, Williams JL

GBSX 1.3 – Experimental Design and Demultiplexing Genotyping by Sequencing Experiments

GBSX 1.3

:: DESCRIPTION

GBSX is a package of tools to first aid in experimental design, including choice of enzymes and barcode design. Secondly, it provides a first analysis step to demultiplex samples using in-line barcodes, providing fastq files that can easily be plugged into existing variant analysis pipelines.

::DEVELOPER

GBSX team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Perl
Java

GBSX

:: MORE INFORMATION

Citation

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments.
Herten K, Hestand MS, Vermeesch JR, Van Houdt JK.
BMC Bioinformatics. 2015 Mar 6;16(1):73.

Cypiripi – Exact Genotyping of CYP2D6 using High-throughput Sequencing data

Cypiripi

:: DESCRIPTION

Cypiripi is a tool for exact genotyping of CYP2D6 using High Throughput Sequencing Data.

::DEVELOPER

Lab for Computational Biology at SFU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Cypiripi

:: MORE INFORMATION

Citation

Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data.
Numanagić I, Malikić S, Pratt VM, Skaar TC, Flockhart DA, Sahinalp SC.
Bioinformatics. 2015 Jun 15;31(12):i27-i34. doi: 10.1093/bioinformatics/btv232.

GIGI-Check 1.06 – Detection of Mendelian Consistent Genotyping Errors

GIGI-Check 1.06

:: DESCRIPTION

GIGI-Check is a C++ program to detect Mendelian consistent genotyping errors of dense markers in pedigree data.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

GIGI-Check

:: MORE INFORMATION

Citation:

Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2014)
Detection of Mendelian Consistent Genotyping Errors in Pedigrees.
Genetic Epidemiology 38(4):291-299

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.

WNV Typer – Genotyping of West Nile Viruses

WNV Typer

:: DESCRIPTION

WNV Typer is a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.

::DEVELOPER

Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.
Kolekar P, Hake N, Kale M, Kulkarni-Kale U.
J Virol Methods. 2014 Mar;198:41-55. doi: 10.1016/j.jviromet.2013.12.012.

AgileGenotyper 20130204 – SNP Genotyping File data from SAM files containing Exome Sequence data

AgileGenotyper 20130204

:: DESCRIPTION

AgileGenotyper will create a pseudo-microarray SNP genotyping file from an ordered SAM file containing exon sequence data. The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Microsoft .NET framework version 2.0

:: DOWNLOAD

AgileGenotyper

:: MORE INFORMATION

GPHMM 1.4 – Unravel Tangled Genotyping Data generated from Tumor Samples

GPHMM 1.4

:: DESCRIPTION

GPHMM (Global Parameter Hidden Markov Model) is a novel statistical method dedicated to identify copy number alteration and loss of heterozygosity (LOH) in tumor samples using whole genome SNP arrays.

::DEVELOPER

HI_Lab @ USTC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsX/Linux
Matlab

:: DOWNLOAD

GPHMM

:: MORE INFORMATION

Citation

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays.
Li A, Liu Z, Lezon-Geyda K, Sarkar S, Lannin D, Schulz V, Krop I, Winer E, Harris L, Tuck D.
Nucleic Acids Res. 2011 Jul;39(12):4928-41. doi: 10.1093/nar/gkr014.

AlphaAssign 1.1 – Parentage Assignment with Genotyping-by-sequencing data

AlphaAssign 1.1

:: DESCRIPTION

AlphaAssign is a parentage assignment algorithm. This program uses a likelihood based model to determine the sire of an individual based on a list of potential sires. AlphaAssign differs from other parentage assignment algorithms by having the option to use phase information to determine parentage.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/ Windows
Python

:: DOWNLOAD

AlphaAssign

:: MORE INFORMATION

Citation

Whalen A, Gorjanc G, Hickey JM.
Parentage assignment with genotyping-by-sequencing data.
J Anim Breed Genet. 2019 Mar;136(2):102-112. doi: 10.1111/jbg.12370. Epub 2018 Dec 13. PMID: 30548685; PMCID: PMC6392119.