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    31 repositories

    • Ratatosk

      Public
      Hybrid error correction of long reads using colored de Bruijn graphs
      C++
      •
      BSD 2-Clause "Simplified" License
      •8•108•4•0•Updated Jan 17, 2026Jan 17, 2026

    • Emblask

      Public
      Dual assembly pipeline for ONT and Illumina reads
      Nextflow
      •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • weaver

      Public
      Short read pangenome reference mapper
      0•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • nf-weaver

      Public
      Nextflow workflows for mapping reads with weaver
      Nextflow
      •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • graphtyper

      Public
      Population-scale genotyping using pangenome graphs
      bioinformaticsgraphgenetics
      bioinformaticsgraphgeneticsvariantsgenotypedecode-genetics
      C++
      •
      MIT License
      •22•197•75•0•Updated Jan 9, 2025Jan 9, 2025

    • gnonadd

      Public
      R
      •
      Other
      •0•2•0•0•Updated Dec 18, 2024Dec 18, 2024

    • PalssonEtAl_Nature_2024

      Public
      Supplementary data for Nature publication: Complete human recombination maps
      0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • svimmer

      Public
      Structural variant merging tool
      Python
      •9•57•7•1•Updated Aug 23, 2024Aug 23, 2024

    • Stefanssonetal-Nature-Genetics-2024

      Public
      R
      •
      MIT License
      •0•2•1•0•Updated Jun 19, 2024Jun 19, 2024

    • popSTR

      Public
      PopSTR - A Population based microsatellite genotyper
      C++
      •
      GNU General Public License v3.0
      •9•32•5•0•Updated Oct 23, 2023Oct 23, 2023

    • proteomics_comparison

      Public
      Supplementary code for the article "Large-scale plasma proteomics comparisons through genetics and disease associations"
      Python
      •0•4•0•0•Updated Aug 16, 2023Aug 16, 2023

    • mDNM_analysisAndData

      Public
      Scripts for mDNM analysis and the data the analysis was run on.
      R
      •
      MIT License
      •0•1•0•0•Updated Aug 1, 2023Aug 1, 2023

    • NCOurd

      Public
      Modelling Length Distributions of NCO Events and Gene Conversion Tracts
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Aug 16, 2022Aug 16, 2022

    • popvcf

      Public
      Lossless VCF compression
      C++
      •1•21•1•0•Updated Mar 4, 2022Mar 4, 2022

    • LRcaller

      Public
      C++
      •
      Other
      •5•16•3•0•Updated Jan 10, 2022Jan 10, 2022

    • LRS_SV_sets

      Public
      VCF files of SVs using long-read sequencing (LRS).
      2•22•1•0•Updated Dec 17, 2021Dec 17, 2021

    • sv-merger

      Public
      Forms SV cliques using the CAST (Cluster Affinity Search Technique) algorithm.
      Python
      •2•9•0•0•Updated Nov 29, 2021Nov 29, 2021

    • COVID19_reconstruction_iceland

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Jun 10, 2021Jun 10, 2021

    • graphtyper-pipelines

      Public
      Recommended Graphtyper pipelines
      Shell
      •
      GNU General Public License v3.0
      •4•15•2•0•Updated Feb 22, 2021Feb 22, 2021

    • SquiggleSV_samplerun

      Public
      Sample run with test data on the squigglesv branch of Nanopolish
      0•1•0•0•Updated Feb 3, 2021Feb 3, 2021

    • read_haps

      Public
      Detects human contamination in bam files
      C++
      •
      Other
      •1•16•0•0•Updated Sep 10, 2020Sep 10, 2020

    • BamHash

      Public
      C++
      •
      GNU General Public License v3.0
      •8•36•8•0•Updated Aug 13, 2020Aug 13, 2020

    • BamQC

      Public
      Quality control for BAM files
      C++
      •0•4•0•0•Updated Jan 27, 2020Jan 27, 2020

    • nanopolish

      Public
      Signal-level algorithms for MinION data
      C++
      •
      MIT License
      •160•0•0•0•Updated Dec 10, 2019Dec 10, 2019

    • scrappie

      Public
      Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
      C
      •
      Other
      •25•1•0•0•Updated Nov 22, 2019Nov 22, 2019

    • SViper

      Public
      Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
      C++
      •8•4•0•0•Updated Nov 21, 2019Nov 21, 2019

    • Nanopolish_SVsquigglefilter

      Public
      Extension to nanopolish to compute alt-ref allele likelihood differences for suggested SVs using the squiggles of reads involved.
      C++
      •
      MIT License
      •0•1•0•0•Updated Jun 20, 2019Jun 20, 2019

    • bamLiftOver

      Public
      C++
      •0•3•0•0•Updated Dec 13, 2018Dec 13, 2018

    • SeqAnHTS

      Public
      A SeqAn 2.1 fork that can use htslib
      C++
      •
      Other
      •0•1•0•0•Updated Dec 12, 2018Dec 12, 2018

    • bamShrink

      Public
      Filter for BAM-files
      C++
      •0•5•1•0•Updated Sep 25, 2017Sep 25, 2017
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