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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Has reproduction · 43
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
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.
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Has reproduction · 90
The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.
PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups
The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application
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Full-text index only
Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.
PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups
GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage
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Has reproduction · 80
GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.
PMID 33193602 · PMC7541957 · Frontiers in genetics · 2020 · 8 claims · 5 setups
GenomeChronicler is, to the authors' knowledge, the first pipeline that can be run offline or in the cloud to generate non-disease-limited personal genomics reports from whole genome or whole exome sequencing data.
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Has reproduction · 79
Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.
PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups
AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies
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Has reproduction · 51
Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer.
PMID 36140751 · PMC9498802 · Genes · 2022 · 7 claims · 6 setups
Clair3 and Human-SNP-wf (which incorporates Clair3) achieved the highest performance among the six variant callers tested.
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Has reproduction · 64
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.
PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups
Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)
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Has reproduction · 100
poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.
PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups
poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data
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Has reproduction · 75
Sequencing of human genomes with nanopore technology.
PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups
A novel single-sample, reference panel-free, read-based phasing algorithm built on the STITCH model improves nanopore SNV calling from modest baseline levels.