Search Results for "snp"
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Showing 7 open source projects for "snp"
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QSdpR
Viral Quasispecies Reconstruction software based on QSdpR algorithm
This is a viral quasispecies reconstruction software for quasispecies assembly problem on mRNA viruses, which is based on a correlation clustering approach and uses semidefinite optimization framework. The software accepts a reference genome, a NGS read set aligned to this reference and set of SNP locations in the form of a vcf file and outputs an optimal set of reconstructed species genomes which describes the underlying viral population. -
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SPRITE
Parallel SNP detection pipeline
SPRITE is an open-source software package providing a parallel implementation of the Single Nucleotide Polymorphisms (SNP) detection genomic data analysis workflow. It consists of three tools: PRUNE for read alignment, SAMPA for intermediate file processing, and PARSNIP for parallel SNP calling. -
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DNAA is the DNA analysis package, for analyzing next-generation post-alignment whole genome resequencing data. Specifically, DNAA is able to find structural variation, SNP and indel variants, as well as evaluating the mapping and data quality.
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bint
Converts intensity text files to binary for fast subsetting
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 grep/awk'ing the text files exported from the genotyping run (e.g. Illumina final report files). bint converts the text representation of the intensity float data to into a IEEE754 indexed binary file... -
PMG Low-Code Automation PlatformPMG is a low-code software platform that allows users to configure automation solutions and business applications to drive digital transformation initiatives. From streamlining business processes through automation, to integrating existing systems and filling in point solution functionality gaps, to delivering a collaborative workspace and unified user experience – PMG’s low-code platform does it all without coding. Business users as well as IT resources are empowered to configure, deploy, and maintain solutions that meet their company’s specific needs.
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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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Utility to convert PED genome file into RAW SNP format. Creates multiple files per person. Supports big files. The same conversion utility has been included into "aisconvert" toolkit, so this project is rather deprecated.
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Avenzoar is a one-year exploration of renal cell carcinoma morphology and its related single nucleotide polymorphisms (SNPa) as a method of automating diagnosis of cancer by using a computer-aided decision tree controlled by analytical statistics.
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