Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.
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Updated
Jun 4, 2024 - C++
Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.
Proteogenomics database-generation tool for protein haplotypes and variants
Kernelized HAplotype-based MIXed model association mapping (KHAMIX)
Docs for AmpliPiper, developed by @nhmvienna
ClairS - a deep-learning method for long-read somatic small variant calling
A data and code repository for the paper of the same name.
Smart and Accurate Polishing of Phase Haplotypes Integrating Read Enhancements (SAPPHIRE)
Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
A novel bioinformatics tool in Java to build phased long alleles of STR+SNP+InDel from VCF file
Scripts to automate the phasing with several tools
A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.
A collection of WDL bioinformatic workflows to benchmark markers coming from different pipelines using linkage map quality as a diagnosis.
A python program that uses ReadBack phased haplotypes in population of samples and returns extended haplotype blocks.
Chromosome Overlap: code accompanying "Refining the genetic risk of breast cancer with rare haplotypes and pattern-mining" by Letsou et al. DOI: 10.26508/lsa.202302183
Bayesian haplotype-based mutation calling
PBWT-based algorithm for identifying all Maximal Perfect Haplotype Blocks with Wildcards
A set of functions for filtering erroneous sequences in eDNA metabarcoding data
Haplotype Fixation Index for crop populations with homozygous nature, such as rice
TFM_AliciaAranda_QApckg
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