genotyping-by-sequencing

There are 2 repositories under genotyping-by-sequencing topic.

• dantaki / SV2

  Support Vector Structural Variation Genotyper

  structural-variationgenotyping-by-sequencinggenotypemachine-learningde-novo-mutationbioinformatics
  Language:Python 58

• thierrygosselin / radiator

  RADseq Data Exploration, Manipulation and Visualization using R

  radseqradseq-dataimputationgenotype-likelihoodsfiltergeneticsmissingnessoutliersgenomicsgenomic-data-analysisgenomics-visualizationgbsgenotyping-by-sequencingvisualizationoutliers-detectionheterozygosityparalogsartifacts-detectionbatch-effectsnormalization
  Language:HTML 57

• thierrygosselin / stackr

  stackr: an R package to run stacks software pipeline

  radseqradgenotype-likelihoodsfiltergeneticsgenomicsgenomic-data-analysisgenomics-visualizationradseq-datagbsgenotyping-by-sequencingstackr
  Language:R 26
• polyRAD

  lvclark / polyRAD

  Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

  bioinformaticsrdna-sequencinggenotyping-by-sequencinggenotype-likelihoodsrad-seqrad-sequencingsnp-genotypinghacktoberfest
  Language:HTML 24
• assigner

  thierrygosselin / assigner

  Population assignment analysis using R

  genomicsdatascienceassignment-analysisassignmentradseqradseq-datafstgbsgenotyping-by-sequencing
  Language:R 17

• Gregor-Mendel-Institute / SNPmatch

  A simple python library to identify the most likely strain from the population

  genotypesnpsaragenogenotyping-by-sequencinggenotyping1001genomesarabidopsispipelinesnpmatch
  Language:Python 9
• NeuroPGx

  Andreater / NeuroPGx

  A clinical decision-support system to identify pharmacogenomics profiles based on subjects genotype of five core genes. The paper has been published in the Journal of Personalized Medicine.

  genomicsbioinformaticspharmacogenomicsmetabolomicsgenotyping-by-sequencingclinical-decision-supportneuroscience
  Language:R 7

• Cristianetaniguti / Reads2Map

  A collection of WDL bioinformatic workflows to benchmark markers coming from different pipelines using linkage map quality as a diagnosis.

  genotyping-by-sequencinghaplotypeslinkage-mappingpipelinesvariant-callingwdl
  Language:WDL 7

• Hanryi / MarkerTech

  An advanced genotyping pipeline by next-generation sequencing (NGS) technology

  pythonpipelinegenomicsgenotyping-by-sequencingsnpsindels
  Language:Python 4

• AlgoLab / MALVIRUS

  A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)

  genotypinggenotyping-by-sequencingalignment-freesars-cov-2virologykmer
  Language:JavaScript 2

• g-pacheco / PigeonBreedsGenomics

  🕊 This repository is associated with the manuscript Pacheco et al. (2020).

  animal-breedinggenotyping-by-sequencingpigeon-breedspopulation-genomics
  Language:R 1

• petersm3 / buildtassel3

  Wrapper scripts for TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) and UNEAK (Universal Network Enabled Analysis Kit) v3.0 Genotyping by Sequencing (GBS) analysis pipelines

  gbsgenotypinggenotyping-by-sequencinguneaktasselsnpsnps
  Language:Shell 0

• rbpisupati / nf-snpmatch

  Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)

  nextflowsnpmatcharagenogenotyping-by-sequencingarabidopsis1001genomes
  Language:Nextflow 0

• wchehadeh / HIV-CODEHOP

  CODEHOP-mediated genotyping of HIV-1

  articgenotyping-by-sequencinghiv-1minion
  0

• CarolinaPB / gbs-genetic-fitness

  pipeline to perform gbs and genetic fitness analysis

  gbsscaffoldingbioinformaticspipelinesnakemakesnakemake-pipelinegenotyping-by-sequencing
  Language:Shell

• dmgatti / GBRS_Tutorial

  Tutorial for Genotyping by RNA Sequencing (GBRS), which quantifies transcripts via RNASeq and genotypes the samples using SNPs in transcripts.

  gbrsgenotyping-by-sequencingrnaseq
  Language:Shell

• natforsdick / Weta_GBS

  Repo containing all scripts associated with Poor Knights giant wētā population genomic analysis from GBS data

  genotyping-by-sequencingpopulationgenetics
  Language:Shell