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

covigator

CoVigator - Monitoring SARS-CoV-2 mutations

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.

EasyFuse

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

neofox

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

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.

splice2neo

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

TCLP

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

tronflow-alignment

Nextflow pipeline for BWA, BWA2 and STAR alignments

tronflow-mutect2

Nextflow pipeline for Mutect2 somatic variant calling best practices

vafator

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

TRON-Bioinformatics/EasyFuse

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

TRON-Bioinformatics/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.

TRON-Bioinformatics/neofox

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

TRON-Bioinformatics/tronflow-mutect2

Nextflow pipeline for Mutect2 somatic variant calling best practices

TRON-Bioinformatics/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.

TRON-Bioinformatics/covigator

CoVigator - Monitoring SARS-CoV-2 mutations

TRON-Bioinformatics/tronflow-alignment

Nextflow pipeline for BWA, BWA2 and STAR alignments

TRON-Bioinformatics/splice2neo

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

TRON-Bioinformatics/vafator

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

TRON-Bioinformatics/TCLP

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

TRON-Bioinformatics/tronflow-vcf-postprocessing

A Nextflow variant normalization pipeline based on vt and bcftools

TRON-Bioinformatics/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.

TRON-Bioinformatics/tronflow-hla-hd

A Nextflow workflow for HLA typing using HLA-HD

TRON-Bioinformatics/easyquant

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

TRON-Bioinformatics/variantmedium

TRON-Bioinformatics/milneo_analysis

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

TRON-Bioinformatics/nf-core-modules

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

TRON-Bioinformatics/nf-core-test-datasets

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

TRON-Bioinformatics/splicing_manuscript_scripts

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

TRON-Bioinformatics/tronflow

TronFlow documentation

TRON-Bioinformatics/tronflow-copy-number-calling

A nextflow workflow for copy number calling

TRON-Bioinformatics/tronflow-haplotype-caller

A nextflow pipeline implementing GATK's HaplotypeCaller best practices

TRON-Bioinformatics/tronflow-test-data

A collection of test data for our TronFlow pipelines

TRON-Bioinformatics/vcf2neofox

TRON-Bioinformatics/bioconda-recipes

Conda recipes for the bioconda channel.

TRON-Bioinformatics/covigator-analysis

Some data analysis and prototypes from the CoVigator project

TRON-Bioinformatics/covigator-intrahost-model

TRON-Bioinformatics/curahack

TRON-Bioinformatics/easyfuse-src

EasyFuse source code to build python package

TRON-Bioinformatics/env2sif

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