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 · 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 · 82
Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.
PMID 35680918 · PMC9184574 · Scientific data · 2022 · 8 claims · 8 setups
Four reference samples (Sample A, Sample B, Sample C, Sample Spike-in/AC5) were developed with large numbers of high-confidence positive and negative small variant positions to serve as known content for oncopanel performance assessment.
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Has reproduction · 42
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.
PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups
KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.
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Has reproduction · 50
rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.
PMID 34110280 · PMC8461470 · Microbial genomics · 2021 · 8 claims · 8 setups
rMAP is a pipeline capable of profiling the resistomes of ESKAPE pathogens using Illumina WGS data
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Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning divergent (cross-subspecies) sequence data detects substantially more SNVs than aligning to a same-subspecies reference, indicating reference/assembly bias in variant calling.
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Has reproduction · 54
EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.
PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups
EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology
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Has reproduction · 100
A workflow reproducibility scale for automatic validation of biological interpretation results.
PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups
Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged
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Has reproduction · 89
Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.
PMID 31913291 · PMC6949293 · Scientific data · 2020 · 6 claims · 7 setups
The Accel-Amplicon CFTR panel generates sequencing data with high coverage depth and near 100% on-target reads.
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Has reproduction · 71
polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.
PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups
polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.