Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.

  PMID 42097292 · PMC13188985 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

  Full-text index only

  StrainMake is a Snakemake-based, Conda-managed workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data.

  cami high-quality recovered gut metagenome metagenomic mag

• Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

  PMID 41252442 · PMC12758600 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

  Full-text index only

  Cleanifier is a fast, memory-frugal alignment-free tool for detecting and removing human contamination using gapped k-mers (spaced seeds) and a human pangenome index.

  genomes genome cami t2t host-contamination pangenome