Microassembly based somatic variant caller for NGS data

🌲 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

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

DNA sequencing analysis notes from Ming Tang

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

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

Clone identification from single-cell data

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

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.

Multi-sample somatic variant caller

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Transposon Insertion Finder - Detection of new TE insertions in NGS data

knowledge-based genotyping of cancer hotspots from the tumor BAM files

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

Snakemake workflow for somatic mutation detection without matched normal samples

Tumor-only variant calling

Transposable Element Finder - Detection of active transposable elements from NGS data

Explore and filter structural variant calls from Lumpy and Delly VCF files

An R package for mutation quality control of cancer genomic sequening dataset

Datasets and analysis results released with the REVOLVER package for Cancer Evolution.