Illumina

The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis

This script imports multiple fields of data from Illumina Final Report text files. It can be used to just import genotype data, or multiple real-valued columns such as B-Allele Frequency, or Log R Ratios. The user can choose from all fields found in the text file and select which ones should be...

AA seriesA ofA programsA designedA forA accurateA andA highA speedA alignmentA ofA shortA readsA toA referenceA genomes.A NovelA featuresA includeA theA useA ofA baseA qualitiesA inA theA readsA andA ambiguousA nucleotideA codesA inA theA referenceA sequencesA forA alignment. KeyA features: -...


Platforms: Mac

CNVision is a small, simple application designed to simplify CNV analysis of Illumina genotyping data. It will simplify all stages of predicting and analyzing CNVs, from running prediction algorithms and combining their results to visualizing the raw data and designing qPCR primers for...


Platforms: Windows

Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker. For information on accessing B Allele Frequencies for Illumina data,


Platforms: Mac

Welcome to the SRMA home page. SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed...


Platforms: Mac

GNomEx is Genomic LIMS and Analysis Project Center designed by the Huntsman Cancer Institute for use by microarray and next generation sequencing core facilities and large research laboratories. KWs: Illumina, Affymetrix, Agilent, MAGE, MySQL/Flex...


Platforms: Windows

The advent of massively parallel sequencing technologies has fundamentally changed the study of genetics. New platforms like the Illumina GAIIx and the Roche GS yield unprecedented levels of sequencing throughput. The analysis and interpretation of data from next-generation sequencing platforms...


Platforms: Windows

bint was written for the purpose of obtaining subsets of intensity data from genotyping assays. Either the X & Y intensities for creating cluster plots or Log R Ratio and B Allele Frequencies for CNV detection. Extracting the data for individual SNP/CNV markers or individual samples was slow...


Platforms: Windows, Mac, BSD, Linux

VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data.


Platforms: Windows, Mac, Linux