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nf-core/variantbenchmarking is designed to evaluate and validate the accuracy of variant calling methods in genomic research. Initially, the pipeline is tuned well for available gold standard truth sets (for example, Genome in a Bottle and SEQC2 samples) but it can be used to compare any two variant calling results. The workflow provides benchmarking tools for small variants including SNVs and INDELs, Structural Variants (SVs) and Copy Number Variations (CNVs) for germline and somatic analysis.

Noodle is a public, read-only web application for semantic discovery and exploration of biomedical literature sourced from PubMed, Europe PMC, and OpenAlex. It accepts natural-language research questions and presents ranked publications together with gene, genetic variant, and phenotype views. Publication pages provide provenance, identifiers, source links, indexed concepts, and navigable semantic-neighbourhood graphs. The companion Noodle Biomedical Literature Discovery MCP exposes the same public discovery domain through a read-only, source-linked Model Context Protocol interface with bounded citation and semantic graph traversal. Semantic proximity, citation distance, co-mention, and search rank are discovery signals and do not establish scientific evidence, causality, diagnosis, or treatment.

Inflexa is an open-source, agentic orchestration platform for computational biology and translational medicine. It is designed to assist researchers in analyzing multi-omics, cheminformatics, and imaging data by reading published literature, designing multi-step analysis plans, and executing experiments with full reproducibility.

Software comprehensive pan-genome variant detection pipeline to identify genetic variations across diverse populations. It supports execution on both local machines and Sun Grid Engine (SGE) clusters. Leveraging pan-genome references, the tool enables high-precision detection of Single Nucleotide Variants (SNVs), INDELs.

Tool for converting raw DNA data files between 23andMe, AncestryDNA, MyHeritage, and FamilyTreeDNA formats.

k-mer counting, filtering, and graph traversal.

Standalone C library for assembling Illumina short reads in small regions

This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.

Reactr is an modularized, Snakemake workflow for automated, species-agnostic characterization of gene families from sequence to experimental design. Given a query protein sequence and NCBI taxonomy IDs (or RefSeq assembly accessions), reactr retrieves genomic data and runs comprehensive analysis across 4 integrated tiers: (1) evolutionary analysis, including homolog detection, domain-based clustering, multiple sequence alignment, and phylogenetic inference; (2) synteny and selection analysis, detecting collinear blocks and calculating Ka/Ks ratios; (3) structural and regulatory characterization, including motif discovery, chromosomal mapping, biochemical property prediction, subcellular localization prediction, and promoter analysis; and (4) experimental design tools, generating PCR primers and scored CRISPR gRNAs for lab validation. Reactr bridges computational prediction and experimental validation, thus enabling rapid transition from genomic discovery to functional studies.

WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.