polyploid

There are 1 repository under polyploid topic.

• edgardomortiz / vcf2phylip

  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

  vcfsnpsphylipalignmentphylogeneticsnexusbinarysnappfastaoutgroupconvert-snpsvcf-filesphylogenetic-analysisvcf-formatphylip-matrixhaploiddiploidpolyploid
  Language:Python 314

• tanghaibao / allhic

  Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

  contigsgenetic-algorithmgenome-assemblygenome-scaffoldinggenomicsgolangheterozygoushi-cinter-contig-linkslachesispipelinepolyploid
  Language:Jupyter Notebook 60

• OmarOakheart / nPhase

  Ploidy agnostic phasing pipeline and algorithm

  polyploidphasingbioinformaticsbioinformatics-pipeline
  Language:Python 45

• wangyibin / CPhasing

  C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

  genome-assemblyhaplotype-assemblypolyploidpore-cscaffoldingphasingultra-longdiploidhaplotype-resolved-assemblyassemblygenomegenome-assemblerhi-chichifichifi-c
  Language:Python 32
• MAPpoly

  mmollina / MAPpoly

  Genetic maps in autopolyploids

  polyploidpolyploidypolyploid-genetic-mapping
  Language:R 28

• tanghaibao / mcscan

  Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

  syntenycomparative-genomicsgenomicsevolutionpolyploid
  Language:C++ 21

• gabrielgesteira / QTLpoly

  R package for random-effect multiple QTL mapping in autopolyploids

  polyploidqtl-mapping
  Language:R 6

• jeffersonfparil / poolgen

  Quantitative and population genetics analyses of populations, pools, half-sib/full-sib families, and polyploids

  pool-seq-datapool-sequencingquantitative-geneticsfamiliespolyploidpopulation-geneticsallele-frequenciesbioinformaticsevolutiongenomic-selectiongwasheterozygositysite-frequency-spectrumgenomic-prediction
  Language:Rust 3

• plantarum / flowPloidy-old

  This repo is deprecated. Use https://github.com/plantarum/flowPloidy instead!

  bioconductorflow-cytometrypolyploidevolution
  Language:R 2

• wangyibin / collapse_rescue

  Method for rescuing collapsed contigs.

  genome-assemblygenome-scaffoldinggenomicshi-cpolyploid
  Language:Python 2

• ammodramus / tsmc

  triploid SMC inference method

  coalescentpolyploidasexual-reproduction
  Language:C 1

• mmollina / B2721_map

  This repository hosts codes and analytic procedures for the article "The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. ‘Atlantic’-derived F1 population" by Pereira et al. (2020)

  polyploid
  Language:R 1

• mchizk1 / UA_Fruit_Breeding

  This repository serves to document, share, and collaborate on scripts used in the University of Arkansas fruit breeding lab.

  horticulturebioinformaticsresearchplant-breedingphenotypingpolyploid
  Language:R 0

• alicefornasiero / IOMAP-3

  This repository contains the main codes used in the manuscript: "Oryza genome evolution through a tetraploid lens"

  genome-assemblykmer-coveragespangenome-analysisoryzapolyploid
  Language:Shell

• DomBennett / Project-cluster

  :hibiscus: Short pipeline for counting number of clusters across .sam files

  cdhitclusteringpipelinepolyploid
  Language:Python

• k8hertweck / Callisia

  Preliminary mapping and SDM

  polyploidrspecies-distribution-modellinghistorical-data
  Language:HTML

• pblischak / fluidigm2purc

  Automated processing and haplotype inference for double-barcoded PCR amplicons

  fluidigmhigh-throughput-sequencingphylogenomicspolyploid
  Language:Python