PolyMarker – Fast Polyploid Primer Design Pipeline

PolyMarker

:: DESCRIPTION

PolyMarker is a tool that simplifies the design of genetic markers, a laboratory test to know if certain variant of the genome is present or not in a plant.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Jun 15;31(12):2038-9. doi: 10.1093/bioinformatics/btv069.

PolyMarker 0.9.9 – Polyploid Primer Design

PolyMarker 0.9.9

:: DESCRIPTION

PolyMarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid wheat.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • BioRuby

:: DOWNLOAD

 PolyMarker

:: MORE INFORMATION

Citation

PolyMarker: A fast polyploid primer design pipeline.
Ramirez-Gonzalez RH, Uauy C, Caccamo M.
Bioinformatics. 2015 Feb 2. pii: btv069

GSP – Genome Specific Primers Design in Polyploid Species

GSP

:: DESCRIPTION

GSP is a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome.

::DEVELOPER

GSP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GSP

:: MORE INFORMATION

Citation

GSP: a web-based platform for designing genome-specific primers in polyploids.
Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ.
Bioinformatics. 2016 Mar 9. pii: btw134.

HapTree 1.0 – Polyploid Haplotype Assembly tool

HapTree 1.0

:: DESCRIPTION

HapTree is a polyploid haplotype assembly tool based on a statistical framework.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  HapTree

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Mar 27;10(3):e1003502. doi: 10.1371/journal.pcbi.1003502. eCollection 2014.
HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.
Berger E, Yorukoglu D, Peng J, Berger B

polyHap 2 – Phase Polyploids and Copy Number Regions

polyHap 2

:: DESCRIPTION

polyHap is a program for phasing polyploids and copy number regions. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 polyHap

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 1;26(11):1437-45. doi: 10.1093/bioinformatics/btq157. Epub 2010 Apr 20.
Inferring combined CNV/SNP haplotypes from genotype data.
Su SY1, Asher JE, Jarvelin MR, Froguel P, Blakemore AI, Balding DJ, Coin LJ.

Shu-Yi Su et al.
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
BMC Bioinformatics 2008, 9:513