Bioinformatics Group at TRON - Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz gGmbH

EasyFuse

EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.

seq2HLA

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

neofox

Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors

tronflow-mutect2

Nextflow pipeline for Mutect2 somatic variant calling best practices

covigator-ngs-pipeline

A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

covigator

CoVigator - Monitoring SARS-CoV-2 mutations

tronflow-alignment

Nextflow pipeline for BWA, BWA2 and STAR alignments

splice2neo

R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes

vafator

Annotate variants in a VCF file with technical annotations from one or more BAMs

TCLP

an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression

tronflow-vcf-postprocessing

A Nextflow variant normalization pipeline based on vt and bcftools

tronflow-bam-preprocessing

Nextflow pipeline for the preprocessing of BAM files based on GATK best practices. Marking duplicates, realignment around indels, base quality score recalibration (BQSR) and reporting of metrics are optional to maintain flexibility for different use cases.

tronflow-hla-hd

A Nextflow workflow for HLA typing using HLA-HD

easyquant

Quantification of reads at defined positions to verify custom input sequences.

variantmedium

milneo_analysis

Code related to the manuscript "Multiple instance learning to predict immune checkpoint blockade efficacy using neoantigen candidates"

nf-core-modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nf-core-test-datasets

Test data to be used for automated testing with the nf-core pipelines

splicing_manuscript_scripts

Scripts related to the manuscript "Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates"

tronflow

TronFlow documentation

tronflow-copy-number-calling

A nextflow workflow for copy number calling

tronflow-haplotype-caller

A nextflow pipeline implementing GATK's HaplotypeCaller best practices

tronflow-test-data

A collection of test data for our TronFlow pipelines

bioconda-recipes

Conda recipes for the bioconda channel.

covigator-analysis

Some data analysis and prototypes from the CoVigator project

covigator-intrahost-model

curahack

easyfuse-src

EasyFuse source code to build python package

env2sif

Python script for creating and editing Singularity images on a HPC servers without sudo rights.

vcf2neofox