fritzsedlazeck

NextGenMap

NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows analysing large scale datasets even with increased SNP rates or higher error rates (e.g. caused by specialized experimental protocols) and avoids biases caused by highly variable regions in the genome.

Teaser

A tool to benchmark mappers and different parameters within minutes

nibSV

Kmer based genotyper for short reads.

parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Sniffles

Structural variation caller using third generation sequencing

Spectre

Copy number caller for long read data including SNV utilization

SURVIVOR

Toolset for SV simulation, comparison and filtering

SVCollector

Method to optimally select samples for validation and resequencing

ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

genomescope

Fast genome analysis from unassembled short reads

fritzsedlazeck/Sniffles

Structural variation caller using third generation sequencing

fritzsedlazeck/SURVIVOR

Toolset for SV simulation, comparison and filtering

fritzsedlazeck/Spectre

Copy number caller for long read data including SNV utilization

fritzsedlazeck/parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

fritzsedlazeck/SVCollector

Method to optimally select samples for validation and resequencing

fritzsedlazeck/nibSV

Kmer based genotyper for short reads.

fritzsedlazeck/SURVIVOR_ant

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)

fritzsedlazeck/sge_mummer

Scripts to split reference and run mummer in parallel on an SGE cluster

fritzsedlazeck/BioBricks

A simple framework to simulate parental and admixture offsprings. The framework allows for a benchmark to distinguish inheritance blocks on the offsprings.

fritzsedlazeck/fritzsedlazeck.github.io

My lab github page

fritzsedlazeck/teaching_material

Collection of teaching instructions

fritzsedlazeck/NA12878

Data and analysis for NA12878 genome on nanopore

fritzsedlazeck/SVhound

fritzsedlazeck/TheHumanPangenome

Creation and Toolsets for a Long-Read Trio Based Human Pangenome

fritzsedlazeck/bioconda-recipes

Conda recipes for the bioconda channel.

fritzsedlazeck/freelancer-theme

Jekyll theme based on Freelancer Start Bootstrap theme

fritzsedlazeck/paragraph

Graph realignment tools for structural variants

fritzsedlazeck/tool_collection

A collection of scripts useful for processing NGS data

fritzsedlazeck/truvari

Structural variant comparison tool for VCFs