decontamination

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.

MIST: a metagenomic intra-species typing tool.

🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

An open-source R package containing decontamination pipelines for low-biomass microbiome data

CroCoClean decontaminates species abundance profiles from metagenomic samples affected by cross-sample contamination

Maintained elsewhere. See README.

AIWG training-complete framework — corpus-to-dataset pipeline with SKILL.md agentic surface and optional Python runtime backend. Marketplace plugin for AIWG.

Zero-dependency CLI + library to detect benchmark/eval data contamination against a training corpus via n-gram overlap, flag leaks, and emit a cleaned dataset.

Closed-loop radiation measurement, mapping, planning, and robotic countermeasure simulation with Isaac Sim, Embree, ROS 2, and local LLM control.

A self-instruct style generation pipeline whose real deliverable is the hygiene layer: MinHash dedup, n-gram decontamination, PII scrubbing, language ID.

LaTeX source for the article 'Optimized Workflow Framework in Construction Projects to Control the Environmental Properties of Soil' (Lindh & Lemenkova, Algorithms 2023, 16(6):303).

A workflow intented for genome decontamination of Caligus minimus

Fast, auditable n-gram detection of benchmark contamination in LLM training corpora (Rust-accelerated).

Three-headed host removal for metagenomic data: assembly, profiling and privacy-scrubbed outputs from one run.

A python implementation of the decontam R package for ASV filtering.

Build pipeline, decontamination audit and a 16-check verifier for scientific-chart-qa-17k: 17,070 evidence-grounded chart questions with a 14.5% unanswerable slice.

A self-instruct style generation pipeline whose real deliverable is the hygiene layer: MinHash dedup, n-gram decontamination, PII scrubbing, language ID.