TRON-Bioinformatics/variantmedium

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TRON-Bioinformatics/variantmedium

TRON-Bioinformatics

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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.

splice2neo

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

tronflow-alignment

Nextflow pipeline for BWA, BWA2 and STAR alignments

covigator

CoVigator - Monitoring SARS-CoV-2 mutations

vafator

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

Jupyter Notebook

TCLP

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

tronflow-hla-hd

A Nextflow workflow for HLA typing using HLA-HD

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.

easyquant

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

ArtiFusion

ArtiFusion is a tool to simulate artificial fusion events by modifying a given reference genome. The tool copies parts of the exonic sequence of gene A within the reference genome FASTA sequence into the downstream region of gene B and replaces the copied regions of gene A with Ns. The breakpoints are defined by using a size ratio between gene A and gene B and are always placed on exon-exon junctions. Intronic and intergenic regions remain unchanged. The approach can be used to benchmark fusion detection tools with realistic biological data. In contrast to simulating NGS reads (ART package, https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm), we do not lose the biological relevance of sequencing data.

SV-LRvsSR

A study to compare structural variation (SV) predictions from 10X Genomics linked-reads sequencing (10XWGS) and conventional Illumina short-reads sequencing (cWGS).

omicron-analysis

Analysis code, data and figures on the omicron MHC binding paper

Jupyter Notebook

tronflow-template

A template to develop new TronFlow pipelines

tronflow-strelka2

Strelka2 nextflow pipeline

tronflow

TronFlow documentation

tronflow-lofreq

LoFreq nextflow pipeline

tronflow-haplotype-caller

A nextflow pipeline implementing GATK's HaplotypeCaller best practices

milneo_analysis

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

splicing_manuscript_scripts

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

tronflow-test-data

A collection of test data for our TronFlow pipelines

tronflow-copy-number-calling

A nextflow workflow for copy number calling