Institute of Clinical Molecular Biology

MAGScoT

MAGScoT - a MAG scoring and refinement tool

eagleimp

TOFU-MAaPO

Nextflow pipeline for the analysis of metagenomic short reads.

dragen-variant-calling

Variant calling pipeline for the Illumina Dragen platform

hla

IKMB pipeline to type HLA alleles from NGS data

hybridgwais

Fast epistasis screening software using hardware accelerators (incl. FPGA and GPU)

exome-seq

A best-practice exome analysis workflow.

HLApipePublic

cram2bam

Convert a CRAM file to BAM

deepvariant

Deepvariant end-to-end workflow

finemapping

A Nextflow framework for finemap

nf-template

A template for a creating a new nextflow pipeline project.

phewas-assoc

The IKMB Association Testing Pipeline for PheWAS

vcf2ethnicity

Determine ethnicity from (exome) vcf file (GRCh38)

bacterial-annotation

Annotates bacterial genome assemblies

BloodTypingArray

The software for the Intitutes genotyping array based blood group typing

catch-all

Data management resources for the clinical research unit catch-all.

cfDNA-quantile

checkphase

crc1182

Data management resources for the CRC1182

flye-assembly

Assembles genomes from Pacbio reads using Flye

GP2_dataset_analysis

hybridgwais-fpga

FPGA design files for HybridGWAIS

MMmicrobiomeLab

nf-testdata

Test datasets for nextflow pipelines.

ngs-qc

QC tools for new sequencing runs (FastQC, FastQ Screen, MultiQC Report)

ucpsc-rnaseq

variant-calling

Generic variant calling pipeline for anything other than human

vcf-concordance

Check VCF files against a reference.

vep

Run VEP on any number of VCFs