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).
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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
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.
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MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.
PMID 41585413 · PMC12824462 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups
MoGAAAP is a modular Snakemake pipeline that automates assembly, provisional annotation, and quality assessment (QA) for any diploid eukaryotic organism
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Has reproduction · 67
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.
PMID 36321867 · PMC9805576 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups
GAVISUNK is an open-source pipeline that validates phased diploid HiFi assemblies by assessing concordance of inter-SUNK distances against orthogonal Oxford Nanopore (ONT) reads.
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Has reproduction · 75
A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.
PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups
Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.