snp-genotyping

There are 2 repositories under snp-genotyping topic.

• seppinho / haplogrep-cmd

  HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

  classificatonhaplogroupmtdnangsphylotreesnp-genotyping
  Language:Java 72
• polyRAD

  lvclark / polyRAD

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

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

• pblischak / polyploid-genotyping

  SNP genotyping in polyploids

  snp-genotypingbioinformaticspopulation-geneticsmanuscriptcpp11genotype-likelihoodsrcpp
  Language:C++ 15

• alinja / snipsa

  Tools for analyzing raw DNA test data files. Shows Y chromosome and mitochondrial mtDNA haplogroups. LGPLv3 - use freely but share improvements.

  haplogroupmtdnamtdna-haplotypessnpsnp-genotyping
  Language:Python 10

• gear-genomics / ancient

  Ancestry inference with convolutional neural networks

  gear-genomicsancestrysequencingsnp-genotypingancestry-researchconvolutional-neural-networksmachine-learningtensorflow
  Language:Vue 9

• lmc297 / SNPBac

  SNP and variant calling pipeline for bacteria

  variant-callingsnp-genotypingbacterial-genomes
  6

• igsr / igsr_analysis

  This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data

  pythonjupyter-notebookperlsnp-genotypingsnp-datapipelinesrna-seqnextflow-pipelines
  Language:Jupyter Notebook 4

• y9c / cpup

  Convert mpileup format to base count tsv table

  bioinformaticsmutationsmpileupsamtoolsrna-modificationssnp-genotypingdna-modifications
  Language:C++ 3

• samleenz / rnaseq-variant-gatk

  Variant calling + processing pipline using GATK based in Snakemake

  gatksnakemakerna-seqsnp-genotyping
  Language:Python 2

• UDC-GAC / mpi3snp

  GWAS third-level epistatic search tool for cluster architectures

  gwassnpsnp-genotypingbioinformaticsmpithreadingparallelismcudagpuepistasis
  Language:C++ 2

• kelly-sovacool / tiger_salamander_project

  SNP pipeline using Snakemake for the Weisrock Lab's Tiger Salamander project.

  snakemakebioinformaticspythonsnp-genotypinghaplotypespopulation-genetics
  Language:Python 1

• ramesh8v / chad_db-BRIL

  Wheat BRIL database created using FLASK server side, angularjs is heavily used at front end

  flaskangularjswheatbrilqtl-mappingsnp-genotyping
  Language:Python 1

• Vvitali / DNAexplorer

  DNA explorer - app for observing decrypted DNA-chains in digital format, app show information about single nucleotide polymorphisms, and provide a brief describtion - it may helps to determine if you have certain genetic predisposition to diseases, and show hidden information encoded in your DNA (your ancestries, phenotypes, predisposition to sport)

  dnarsidsnpssnpsnp-genotypingjavascriptnodejs
  Language:HTML 1

• BaccarelliLab / Main

  Guide for the Baccarelli Lab GitHub

  epigenomicsmethylationillumina-datakernel-regressionsnp-genotypingsnpscolumbia-universitydna-methylationepitranscriptomicsepigeneticspublichealthmachinelearning-rdata-analysistoxicologyenvironmental-exposureshealthepidemiology-analysisr-programming
  0

• eacooper400 / RAD_Pipeline_Info

  Bioinformatics Pipeline for dRADseq Data

  bioinformatics-pipelineradseq-datasnp-genotypingdenovo-assembly
  Language:Perl 0

• gabrielkg / croissant

  Fast and simple haplotype counting.

  genomicshaplotypesalignmentsnp-genotyping
  Language:Scala 0

• josuechinchilla / SNPware

  SNPware is a family of short bash scripts that allows to translate genotypes coded as GCTA or Illuimina Top Strand to AB coding using standard Illumina FinalReport files to create a library of genotype equivalences at each locus.

  genomics-data-setsgenomicssnp-datasnp-genotypingbioinformatics-tool
  Language:Shell 0

• natmurad / variantCalling

  Workflow to perform a Variant Calling Analysis

  bioinformaticsgenomicsngssequencingsnp-genotypingsnpsvariant-calling
  0

• RichardBekoe / Advanced-Computational-Biology-Assignment-1

  Advanced Computational Biology Project Assignment

  r-programmingscientific-computinggeneticsgenomicsgwasmanhattan-plotsnp-genotyping
  Language:R 0

• TC-Hewitt / OatCrownRust

  Custom scripts and workflows used in the genomics and population analysis of oat crown rust (Puccinia coronata f. sp. avenae) preprint (bioRxiv 2023.09.18.557855). All steps performed in Linux environment or R.

  genomic-data-analysisgwasngs-analysisread-alignmentsnp-genotypingsynteny
  Language:Python 0

• wuaipinglab / SARS-CoV-2_early_outbreak

  SARS-CoV-2 early outbreak analysis. Two polymorphism sites 8517 and 27641 (CDS numbering) were found to genotype the early strains.

  phylogeneticssnp-genotyping
  Language:Jupyter Notebook 0

• adiamb / Remove-duplicate-snps-plink

  A python script to remove duplicate snps from plink files and recode the resultant files into plink binaries free of duplicate snps

  duplicategwasplinksnp-genotypingsnps
  Language:Python

• BCCDC-PHL / call-variants

  Align against a reference genome and call variants

  microbial-genomicssnp-genotypingbioinformatics-pipeline
  Language:Python

• Grelot / aker--beetGenomeEnvironmentAssociation

  Codes i wrote for the scientific paper "Predicting genotype environmental range from genome–environment associations"

  genotypegenomesnpssnp-genotypingbeetsecologyrpopulation-geneticspythonbashmetricsenvironmentpopgenomege
  Language:Python

• kgturner / BluebonnetGBS

  Population genetic analyses of seeded and wild populations of Texas bluebonnet (Lupinus texensis).

  population-geneticssnp-genotyping
  Language:Makefile

• ralemy / seq-lava

  Implementation of LAVA algorithm in Seq language.

  dna-sequencingsnp-genotyping
  Language:Python