Repositories list

• graphtyper

  Public
  Population-scale genotyping using pangenome graphs

  bioinformaticsgeneticsgenotype+ 3decode-geneticsgraphvariants

  C++

  •

  MIT License

  •20•177•63•0•Updated Jan 9, 2025Jan 9, 2025

• gnonadd

  Public
  R

  •

  Other

  •0•1•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

• Ratatosk

  Public
  Hybrid error correction of long reads using colored de Bruijn graphs

  C++

  •

  BSD 2-Clause "Simplified" License

  •7•100•0•0•Updated Sep 27, 2024Sep 27, 2024

• svimmer

  Public
  Structural variant merging tool

  Python

  •9•49•5•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•0•0•Updated Aug 16, 2022Aug 16, 2022

• popvcf

  Public
  Lossless VCF compression

  C++

  •1•18•1•0•Updated Mar 4, 2022Mar 4, 2022

• LRcaller

  Public
  C++

  •

  Other

  •3•16•2•0•Updated Jan 10, 2022Jan 10, 2022

• LRS_SV_sets

  Public
  VCF files of SVs using long-read sequencing (LRS).

  2•21•1•0•Updated Dec 17, 2021Dec 17, 2021

• sv-merger

  Public
  Forms SV cliques using the CAST (Cluster Affinity Search Technique) algorithm.

  Python

  •2•8•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•14•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•37•6•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

  •159•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

  •27•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

• chopBAI

  Public
  Chops a bam index file into pieces

  C++

  •

  GNU General Public License v2.0

  •1•5•1•1•Updated Mar 30, 2016Mar 30, 2016