DecodeGenetics

graphtyper

Population-scale genotyping using pangenome graphs

Ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs

svimmer

Structural variant merging tool

BamHash

popSTR

PopSTR - A Population based microsatellite genotyper

LRS_SV_sets

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

popvcf

Lossless VCF compression

LRcaller

read_haps

Detects human contamination in bam files

graphtyper-pipelines

Recommended Graphtyper pipelines

sv-merger

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

bamShrink

Filter for BAM-files

chopBAI

Chops a bam index file into pieces

BamQC

Quality control for BAM files

SViper

Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.

bamLiftOver

proteomics_comparison

Supplementary code for the article "Large-scale plasma proteomics comparisons through genetics and disease associations"

COVID19_reconstruction_iceland

gnonadd

mDNM_analysisAndData

Scripts for mDNM analysis and the data the analysis was run on.

Nanopolish_SVsquigglefilter

Extension to nanopolish to compute alt-ref allele likelihood differences for suggested SVs using the squiggles of reads involved.

scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

SeqAnHTS

A SeqAn 2.1 fork that can use htslib

SquiggleSV_samplerun

Sample run with test data on the squigglesv branch of Nanopolish

Stefanssonetal-Nature-Genetics-2024

nanopolish

Signal-level algorithms for MinION data

NCOurd

Modelling Length Distributions of NCO Events and Gene Conversion Tracts