Discover TRON-Bioinformatics/TCLP Open Source project

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TRON-Bioinformatics

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

EasyFuse

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

Python

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.

Python

neofox

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

Python

tronflow-mutect2

Nextflow pipeline for Mutect2 somatic variant calling best practices

Nextflow

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.

Nextflow

splice2neo

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

tronflow-alignment

Nextflow pipeline for BWA, BWA2 and STAR alignments

Nextflow

covigator

CoVigator - Monitoring SARS-CoV-2 mutations

Python

vafator

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

Jupyter Notebook

tronflow-hla-hd

A Nextflow workflow for HLA typing using HLA-HD

Nextflow

tronflow-vcf-postprocessing

A Nextflow variant normalization pipeline based on vt and bcftools

Shell

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.

Nextflow

easyquant

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

Python

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.

Python

SV-LRvsSR

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

Python

omicron-analysis

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

Jupyter Notebook

variantmedium

tronflow-template

A template to develop new TronFlow pipelines

Nextflow

tronflow-strelka2

Strelka2 nextflow pipeline

Nextflow

tronflow

TronFlow documentation

Nextflow

tronflow-lofreq

LoFreq nextflow pipeline

Nextflow

tronflow-haplotype-caller

A nextflow pipeline implementing GATK's HaplotypeCaller best practices

Nextflow

milneo_analysis

splicing_manuscript_scripts

Shell

tronflow-test-data

A collection of test data for our TronFlow pipelines

tronflow-copy-number-calling

A nextflow workflow for copy number calling

Nextflow

TRON-Bioinformatics/TCLP

TRON-Bioinformatics

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