SNV calling from single cell sequencing

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures.

Flujos de trabajos desarrollados y automatizados en el INMEGEN para el procesamiento de datos genómicos y transcriptómicos.

An ensemble approach to accurately detect somatic mutations using SomaticSeq

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

This page is reserved for NextFlow based Indell Calling Workflow (with Platypus) from DKFZ

Clinical Whole Genome and Exome Sequencing Pipeline

Pipeline for Somatic Variant Calling with WES and WGS data

ClairS - a deep-learning method for long-read somatic small variant calling

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

Tumour-in-Normal Contamination assessment with evolutionary theory.

a Nextflow SNV calling and annotation pipeline based on DKFZ-ODCF/SNVCallingWorkflow

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

R package containing a R Shiny app for somatic genomic variants interpretation and a tool suite to deal with an underlying local structured database.

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.