Data Analysis Tools

Within the GHGA workflow workstream, our bioinformatics team is making steady progress in our effort to provide standardized, comparable, and reproducible omics workflows for the research community. To streamline workflows, the team is improving existing workflows (instead of creating a new process) and aligning with the nf-core  community, curating best practice analytic pipelines. Below, we highlight workflow releases GHGA has been involved in.

If you are starting to use nf-core workflows, we recomment Bytesize - a video tutorial series published by nf-core that covers workflow implementation and nf-core workflows in short and easy to follow snippets!

Benchmarking efforts

Continuous benchmarking against known standards is essential to ensure precision and reliability in variant calling tools and workflows. A recent publication, spearheaded by the Next Generation Sequencing Competence Network (NGS-CN) and GHGA, introduces NCBench, a platform for continuous benchmarking of genomic variant calling workflows. NCBench provides a comprehensive and reproducible benchmarking workflow for the evaluation of small genomic variant callsets in terms of recall, precision, and error patterns. Its continuous and open-source approach eliminates the need for specialised infrastructure, making benchmarking accessible and transparent to the research and diagnostics community but also to patients.

sarek 3.0

Somatic and Germline Variant Calling Methodology (GHGA config) - A coordinated guide on how to call variants given public resources and tool settings

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nanoseq 3.0

Tool for Long Read Sequencing focusing on the Oxford Nanopore technology

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Rare-Disease RNA-seq Analysis (Research Diagnostics) - A tool for RNA-seq processing and interpretation of rare disease outlier detection, that guides researchers towards aberrant RNA events (splicing and expression)

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Platypus based somatic indel calling pipeline with an extensive amount of quality control steps

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Bcftools mpileup based somatic single nucleotide variants calling pipeline with filtering, annotation and result plots

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nf-aceseq Public

Allele-specific copy number estimation for somatic samples

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scrnaseq 2.0

A single-cell RNAseq pipeline for 10X genomics data.

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