genotyping

There are 60 repositories under genotyping topic.

  • mcaller

    Language:Python

  • tblg

    A command-line tool to genotype Mycobacterium tuberculosis lineage from a VCF file

    Language:Python1

  • panvc3

    Variant calling using a pan-genomic reference, version 3

    Language:C++1

  • VarBench

    Benchmarking variant callers for long read data

    Language:Python1

  • genotype_variants

    Project to genotype SNV, INDEL and SV.

    Language:Python1

  • ROHMMCLI

    ROHMMCLI - Flexible HMM based homozygosity predictor.

    Language:Java1

  • breedSimulatR

    R 📦 providing classes and functions to simulate breeding schemes.

    Language:R1

  • PAMmaker

    Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results

    Language:Python1

  • Epigenetics-OA-Risk-Human-Skeletal-Dev

    Methylation and mqtl analysis of the developing knee

    Language:R

  • ddRADseq-for-prokaryota

    This project was written as a first step to apply the ddRADSeq genotyping method to prokaryota. This code is made to dertemine, in silico, the couple of enzymes to apply on a given sequence.

    Language:Python

  • BI-Workshop-miniProjects

    Repository for workshop study projects in Bioinformatics Institute 2023-2024

    Language:Jupyter Notebook

  • ONT-lineage-tracing

    Analyses of Penter, Borji & Nagler et al., 2023

    Language:R

  • genotyping-platform

    genotype prepare for sequencing paltform.

    Language:Python

  • 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

    Language:Shell

  • Z-care

    Graduation Project (2023)

  • SNP_array_comparison

    Running codes and data analysis scripts for SNP array comparison paper

    Language:Shell

  • QA_genotipat_pipeline

    TFM_AliciaAranda_Pipeline

    Language:R

  • Joint-Genotyping-2021-2022

    Joint Genotyping in MIT Fraenkel Lab with ALS Genomics + 1000 Genomes Data

    Language:Jupyter Notebook

  • germinate-training

    Training material for the use of Germinate

    Language:SCSS

  • Mapping-of-a-Novel-Major-Effect-Hessian-Fly-Partial-Resistance-Locus-in-Southern-SRWW-LA03136E71

    Data repository for the paper of the same name.

  • iScanVCFMerge

    Python tool to merge cross-species Illumina iScan genotype data with a reference set of genotypes from a pre-existing source.

    Language:Python

  • amplikate

    📢🎯 Generic typing tool from amplicons and/or in silico PCR

    Language:Perl

  • SNP-Clustering

    Perl software to cluster SNPs based on its genotype.

    Language:Perl

  • sample-fingerprinting

    workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

    Language:WDL