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Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SOAP (RRID:SCR_000689) Copy
http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm
Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: HCLUST (RRID:SCR_009154) Copy
http://www.omicsexpress.com/sva.php
Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.
Proper citation: SVA (RRID:SCR_002155) Copy
http://gaow.github.io/genetic-analysis-software/e-1.html#ehp
Software application that provides variance estimates for haplotype frequency estimates, it allows several kinds of missing information in the genotype data, it also allows for combined genotype data of different pool sizes. This program can be used for testing haplotype-disease associations in case control studies by calculating the likelihood ratio test: 2 log(likelihood for cases) + 2 log(likelihood for controls) - 2 log(likelihood for case+controls). (entry from Genetic Analysis Software)
Proper citation: EHP (RRID:SCR_009170) Copy
https://cran.r-project.org/web/packages/onemap/index.html
Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)
Proper citation: R/ONEMAP (RRID:SCR_009371) Copy
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