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 · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.
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Has reproduction · 95
Sparse and skew hashing of K-mers.
PMID 35758794 · PMC9235479 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 4 setups
Exploiting sparsity and skewed distribution of k-mer minimizers with minimal perfect hashing substantially improves the space/time trade-off of a k-mer dictionary compared to best-known solutions
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Full-text index only
BFAST: an alignment tool for large scale genome resequencing.
PMID 19907642 · PMC2770639 · PloS one · 2009 · 7 claims · 4 setups
BFAST is a new algorithm and freely available software tool for aligning large-scale short-read sequencing data to large reference genomes with user-customizable speed and accuracy
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Has reproduction · 97
CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.
PMID 33667225 · PMC7968741 · PLoS computational biology · 2021 · 8 claims · 7 setups
CRISPRbuilder-TB is a new pipeline that reconstructs MTC CRISPR-Cas loci directly from short SRA reads without requiring genome assembly