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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Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing.
PMID 42178219 · PMC13242794 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups
A high-performance multithreading architecture allows batches of read pairs to be processed independently by a pool of worker threads, scaling efficiently with available hardware.
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rMAP 2.0: a modular, reproducible, and scalable WDL-Cromwell-Docker workflow for genomic analysis of ESKAPEE pathogens.
PMID 41782684 · PMC12955837 · Bioinformatics advances · 2026 · 8 claims · 8 setups
rMAP 2.0 standardizes end-to-end bacterial WGS analysis (QC, trimming, assembly, annotation, AMR/virulence/mobile-element profiling, sequence typing, pangenome inference, phylogenetics) via containerized WDL/Cromwell execution
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Has reproduction · 85
An extensive evaluation of read trimming effects on Illumina NGS data analysis.
PMID 24376861 · PMC3871669 · PloS one · 2013 · 8 claims · 8 setups
Read trimming increases the quality and reliability of downstream NGS analyses (RNA-Seq mapping, SNP identification, genome assembly) while reducing execution time and computational resources.
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Searching for SNPs with cloud computing.
PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups
Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis