haplotypes

There are 0 repository under haplotypes topic.

• luntergroup / octopus

  Bayesian haplotype-based mutation calling

  genomicsvariant-callingbioinformaticsvariantshaplotypessomatic-variantsde-novo-mutationphasingsingle-cell
  Language:C++ 301

• HKU-BAL / ClairS

  ClairS - a deep-learning method for long-read somatic small variant calling

  deep-learninglong-readsnanoporeontsomatic-mutationssomatic-variantsbioinformaticsgenomicshaplotypesphasingsnvsindelsilluminalong-read-sequencingshort-readspacbio
  Language:Python 66

• everestial / VCF-Simplify

  A python parser to simplify and build the VCF (Variant Call Format).

  vcfpython-parservariant-annotationhaplotypesphasingconvertsphase-stitcherphase-extendertableviewvcf-filesvcftoolschrom
  Language:Python 45

• SamStudio8 / gretel

  An algorithm for recovering haplotypes from metagenomes

  bioinformaticshaplotypesmetagenomes
  Language:Python 31

• cbg-ethz / haploclique

  Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

  bioinformaticsc-plus-plushaplotypesquasispecies
  Language:C++ 25

• dancooke / starfish

  Intersect multiple VCF files with haplotype awareness

  vcf-fileshaplotypesintersectioncompare-filesvariant-calls
  Language:Python 22

• vtsyvina / CliqueSNV

  haplotypesilluminaquasispeciespacbiongs
  Language:Java 21

• PlantandFoodResearch / MCHap

  Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

  dna-sequenceshaplotypeshaplotype-assemblyhaplotype-blocksarraynumpybayesian-inferencepolyploidypolyploid-genotypinggenotyping
  Language:Python 18
• edgecase

  LankyCyril / edgecase

  A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

  telomereshaplotypesrepeatsgenomicsbioinformaticsbioinformatics-pipelinegenomics-visualizationlong-readslong-read-sequencing
  Language:Python 15

• luntergroup / bamsplit

  Split a BAM file by haplotype support

  bam-filesvariantsbioinformaticshaplotypes
  Language:Python 15

• PacificBiosciences / minorseq

  Minor Variant Calling and Phasing Tools

  minor-varianthaplotypesphasingdrug-resistancestatisticsnext-generation-sequencinglong-readpacbio
  15

• everestial / phase-extender

  A python program that uses ReadBack phased haplotypes in population of samples and returns extended haplotype blocks.

  haplotypesphase-extenderhaplotype-extensionphase-haplotypesreference-haplotype-panelhaplotype-blockshaplotype-assemblygenome-phasing
  Language:Jupyter Notebook 13

• transbioZI / Gimpute

  An efficient genetic data imputation pipeline

  imputationgenotypingliftovergwasphasinghaplotypes
  Language:R 11

• edgardomortiz / fineRADstructure-tools

  Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

  fineradstructurehaplotypesradseqgbsstructurepyradipyradstacks
  Language:Python 9

• 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 8

• rwk-unil / sapphire

  Smart and Accurate Polishing of Phase Haplotypes Integrating Read Enhancements (SAPPHIRE)

  geneticsgenomicshaplotypecallerhaplotypeswhole-genome-sequencing
  Language:C++ 8

• YaoLi3 / nanopore-methylation

  Long sequencing reads classifier

  oxford-nanoporeepigeneticsdna-methylationhaplotypes
  Language:Python 7

• everestial / phase-stitcher

  a python program to stitch the ReadBack phased haplotypes in F1 hybrids.

  haplotypesf1-hybridsphase-haplotypespopulationphased-genotypeshaplotype-extensionphasinggenome-phasing
  Language:Jupyter Notebook 6

• ProGenNo / ProHap

  Proteogenomics database-generation tool for protein haplotypes and variants

  haplotypesproteogenomicsprotein-database-generation
  Language:Python 5

• ljacquin / khamix

  Kernelized HAplotype-based MIXed model association mapping (KHAMIX)

  association-mappinghaplotype-analysishaplotypesmixed-models-estimationqtlpolygenic-modelsepistasis-modeling
  Language:R 4

• RichardAGoldstein / HaROLD

  Haplotype RecOnstruction using Longitudinal sequencing Data

  genomicshaplotypesmolecular-evolution
  Language:Java 4

• ShujiaHuang / RefHap

  A Reliable and Fast Algorithm for Single Individual Haplotyping

  algorithmdnahaplotypesngs
  Language:Java 4

• tsnorri / vcf2multialign

  Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.

  bioinformaticsvariant-analysishaplotypesfounder-sequences
  Language:C++ 4

• andrea-tango / GenHap

  A Novel Computational Method Based on Genetic Algorithms for Haplotype Assembly

  haplotype-assemblysnpsgenetic-algorithmrochehaplotypesmulticoremaster-slave
  Language:C++ 3

• jamonterotena / Haplotype-based-Pangenome-Wheat-Analysis

  This repository contains the files from my master thesis project required to conduct a whole-genome analysis of haploblocks in wheat based on pairwise comparisons between assemblies. This is based on a previous method (https://doi.org/10.1038/s42003-020-01413-2), but focuses on the the quality of the pairwise comparisons to call haplotypes.

  pangenomicshaplotypeswheatplantbreeding
  Language:R 3

• everestial / PhaseIT

  A pipeline for phasing haploptypes using short readbackphased haplotype blocks in population of samples.

  genomehaplotype-blockshaplotype-extensionhaplotypesphasing
  Language:TeX 2

• everestial / SmallTools

  Collection of several small tools. These tools stay here temporarily and may move to other major repositories as they evolve.

  vcfvcf-fileshaplotypesphasingbedfileprimality-testingprimes
  Language:Python 2

• everestial / TestSwitchErrors

  This is a tutorial that shows how phaseExtender can be used for recursive improvement of haplotype phasing and how to test the phasing quality by measuring switcherrors.

  haplotypespythonr
  Language:Jupyter Notebook 2

• zhuochenbioinfo / VCF2HAP

  Construct gene haplotype with VCF format files and snpEff annotation.

  bioinformaticsgenomicshaplotypesvcf
  Language:Perl 2

• AstraBert / AmpliPiper-docs

  Docs for AmpliPiper, developed by @nhmvienna

  amplicon-sequencingbiodiversitydocumentationgeneticsgenomicshaplotypesjust-the-docsphylogeneticspipeline
  Language:SCSS 1

• inzilico / phase-01

  Scripts to automate the phasing with several tools

  haplotypesphasingsnp
  Language:Python 1

• kelly-sovacool / tiger_salamander_project

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

  snakemakebioinformaticspythonsnp-genotypinghaplotypespopulation-genetics
  Language:Python 1

• XuewenWangUGA / VarSeqStitcher

  A novel bioinformatics tool in Java to build phased long alleles of STR+SNP+InDel from VCF file

  bioinformatics-toolhaplotypesstrvariants
  Language:HTML 1

• zjwinn / HAPLOCATCHER-AN-R-PACKAGE-FOR-PREDICTION-OF-HAPLOTYPES

  A data and code repository for the paper of the same name.

  haplotype-blockshaplotypesmachine-learningr-packagehaplocatcher
  1

• YSKoseki / gmmDenoise

  A set of functions for filtering erroneous sequences in eDNA metabarcoding data

  bioinformaticsdenoisingednametabarcodingasvshaplotypes
  Language:R 0

• AlgoLab / Wild-pBWT

  PBWT-based algorithm for identifying all Maximal Perfect Haplotype Blocks with Wildcards

  bwtpbwthaplotype-blockshaplotypes
  Language:C++