Tag: SNP

SWAP454 46233 – Call SNPs using 454 Read Data

SWAP454 46233

:: DESCRIPTION

SWAP454 is a program for calling SNPs using 454 read data. SWAP454 also includes code for creating improved quality scores for 454 read data that has been incorporated into the algorithm used by 454 Life Sciences.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SWAP454

:: MORE INFORMATION

Citation

Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. 2008.
Quality scores and SNP detection in sequencing-by-synthesis systems.
Genome Research 18: 763–770.

SNPscan – Affymetrix SNP (10K, 50K, 100K, 500K) Visualization

SNPscan

:: DESCRIPTION

SNPscan is a web-accessible tool for the analysis of single nucleotide polymorphism (SNP) array data.

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package
  • Perl
  • Apache

:: DOWNLOAD

  SNPscan

:: MORE INFORMATION

Citation

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.
Ting JC, Ye Y, Thomas GH, Ruczinski I, Pevsner J.
BMC Bioinformatics. 2006 Jan 18;7:25.

SNPduo 1.02a – Pairwise Comparisons of SNP data sets

SNPduo 1.02a

:: DESCRIPTION

SNPduo is designed to provide an analysis of Single Nucleotide Polymorphism (SNP) data between any two individuals. It has been designed based on data exported from Affymetrix CNAT 4.0 or Illumina Beadstudio, as well as data downloaded from the HapMap project. However, provided that the data is formatted correctly SNPduoWeb can analyze any SNP data.

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SNPduo

:: MORE INFORMATION

Citation

PLoS One. 2009 Aug 21;4(8):e6711. doi: 10.1371/journal.pone.0006711.
Visualization of shared genomic regions and meiotic recombination in high-density SNP data.
Roberson ED, Pevsner J.

pediSNP – Locate Meiotic Recombination Sites from SNPs

pediSNP

:: DESCRIPTION

pediSNP is designed to provide an analysis of Single Nucleotide Polymorphism (SNP) data from a pedigree of two generations: two parents with two or more children. It has been designed based on genotype data exported from Affymetrix CNAT 4.0, Illumina Beadstudio, as well as data downloaded from the HapMap project. However, any SNP data is formatted as any one of these three sources, pediSNP can analyze it.

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Locations and patterns of meiotic recombination in two-generation pedigrees.
Ting JC, Roberson ED, Currier DG, Pevsner J.
BMC Med Genet. 2009 Sep 17;10:93. doi: 10.1186/1471-2350-10-93.

kcoeff – Calculate Genetic Relatedness from SNP data

kcoeff

:: DESCRIPTION

kcoeff is a program that accepts SNP genotype data as input and calculates K0, K1, and K2.

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 kcoeff

:: MORE INFORMATION

Citation

Stevens EL, Heckenberg G, Roberson EDO, Baugher JD, Downey TJ, et al. (2011)
Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State.
PLoS Genet 7(9): e1002287. doi:10.1371/journal.pgen.1002287

Tagger – Selection and Evaluation of tag SNPs

Tagger

:: DESCRIPTION

Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

P.I.W. de Bakker, R. Yelensky, I. Pe’er, S.B. Gabriel, M.J. Daly, D. Altshuler (2005)
Efficiency and power in genetic association studies.
Nature Genetics. 37: 1217-1223

shellfish – Parallel PCA and data processing for Genome-wide SNP data

shellfish

:: DESCRIPTION

shellfish carries out a variety of tasks related to principal component analysis of genome-wide SNP data. Unlike other available software, PCA computations can be carried out in parallel (both on a computing cluster running the Sun Grid Engine, and also in the simple case of a machine with multiple processors). In addition to the PCA calculations, it automates the process of data subsetting and allele-matching, using plink and gtool for file format interconversion where necessary. The aim is that tasks that would otherwise require a complex series of shell commands and/or work in R, can be carried out with a single, straightforward, command.

::DEVELOPER

Dan Davison

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • Python

:: DOWNLOAD

 shellfish

:: MORE INFORMATION

McSNP 1.0 – Melting Curve SNP

McSNP 1.0

:: DESCRIPTION

McSNP is a relatively cheap and handy genotyping technique as it is an extension of the RT-PCR technique. It make use of the difference in melting temperature of PCR products for different alleles.

::DEVELOPER

Kung-Hao Liang

:: SCREENSHOTS

McSNP

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 McSNP

:: MORE INFORMATION

Citation

A base-calling algorithm for Tm-shifted melting curve SNP assay.
Liang KH, Fen JJ, Chang HH, Wang HW, Hwang Y.
J Clin Bioinforma. 2011 Jan 20;1(1):3. doi: 10.1186/2043-9113-1-3.

SnpStore 1.0 – SNP and Indel Calling in mapped NGS Sequencing Reads

SnpStore 1.0

:: DESCRIPTION

 SnpStore is a program for SNP and indel calling in mapped next-generation sequencing read data. It features a simple threshold-based model for SNP and indel calling, and a MAQ-like Bayesian model for SNP genotype calling.

::DEVELOPER

Anne-Katrin Emde, Tobias Rausch, Stefan Haas, and Knut Reinert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SnpStore

:: MORE INFORMATION

PS_SNP – Prioritize and Select SNPs for Whole Genome Association Studies with Two-stage Designs

PS_SNP

:: DESCRIPTION

PS_SNP is a novel SNP selection procedure for whole genome association studies with two-stage designs.

::DEVELOPER

Jing Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PS_SNP

:: MORE INFORMATION

Citation

Jing Li.
Prioritize and select SNPs for association studies with multi-stage designs.
J Comput Biol. 2008 Apr;15(3):241-57.