{"repo":"nf-core/oncoanalyser","free":true,"listed":false,"github":"https://github.com/nf-core/oncoanalyser","clone":"git clone https://github.com/nf-core/oncoanalyser.git","description":"A comprehensive cancer DNA/RNA analysis and reporting pipeline","language":"Nextflow","stars":118,"topics":["nextflow","nf-core","pipeline","workflow","cancer","clinical","dna","exome","ngs","panel"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/oncoanalyser is a Nextflow pipeline for the comprehensive analysis of cancer DNA and RNA sequencing data using the WiGiTS toolkit from the Hartwig Medical Foundation. The pipeline supports a wide range of experimental setups: - FASTQ, BAM, and / or CRAM input files - WGS (whole genome sequencing), WTS (whole transcriptome sequencing), and targeted / panel sequencing 1 - Paired tumor / normal and tumor-only samples, and support for donor samples for further normal subtraction - Purity estimate for longitudinal samples using genomic features of the primary sample from the same patient 2 - UMI (unique molecular identifier) processing supported for DNA sequencing data - Most GRCh37 and GRCh38 reference genome builds 1 built-in support for the TSO500 panel with other panels and exomes requiring creation of custom panel reference data 2 for example a primary WGS tissue biospy and longitudinal low-pass WGS ccfDNA sample taken from the same patient Pipeline overview The pipeline mainly uses tools from WiGiTS, as well as some other external tools. There are several workflows available in oncoanalyser and the tool information below primarily relates to the wgts and targeted analysis modes. [!NOTE] Due to the limitations of panel data, certain tools (indicated with below) do not run in targeted mode. - Read alignment: BWA-MEM2 (DNA), STAR (RNA) - Read post-processing: REDUX (DNA), Picard MarkDuplicates (RNA) - SNV, MNV, INDEL calling: SAGE, PAVE - SV calling: ESVEE ","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/oncoanalyser/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}