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).

• Eduomics: a Nextflow pipeline to simulate -omics data for education.

  PMID 41816779 · PMC12972896 · NAR genomics and bioinformatics · 2026 · 8 claims · 4 setups

  Full-text index only

  Eduomics is a Nextflow DSL2 pipeline that automates generation of validated variant-calling and RNA-seq datasets for education while abstracting away technical requirements

  chromosome full simulated exome rna-seq pipeline

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.

  PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups

  Has reproduction · 43

  TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.

  mdr-tb paired-end raw bam whole-genome kraken raw

• A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

  PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

  californensis chromosome pacbio illumina

• Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.

  PMID 41923360 · PMC13070649 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  umi-pipeline-nf is a portable, fully containerized, modular Nextflow DSL2 workflow that generates single-molecule consensus sequences from UMI-tagged nanopore amplicon data and scales linearly from single samples to large cohorts.

  lpa zymo sars-cov-2 nanopore real-time umi