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).

• GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.

  PMID 36321867 · PMC9805576 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups

  Has reproduction · 67

  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.

  chm13 chm1 hg02723 genome sunk haplotype

• Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex.

  PMID 38883333 · PMC11179850 · Horticulture research · 2024 · 7 claims · 7 setups

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  A haplotype-resolved telomere-to-telomere (T2T) genome of plum (P. salicina cv. 'Fengtangli') was assembled into two gap-free haplotypes of 251.25 and 251.29 Mb.

  plum four appm genes pacbio hi-c k-mer

• ANOMALY: a Snakemake pipeline for identifying NuMTs from long-read sequencing data.

  PMID 41647924 · PMC12869244 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

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  ANOMALY is a novel Snakemake pipeline for detecting NuMTs from long-read sequencing data

  simulated real-world matched long-read short-read pipeline

• Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

  PMID 41826793 · PMC13020910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Pre-generated Blacklist exclusion sets were difficult to reproduce due to sensitivity to input BAM data, aligner choice, and read length

  hg38 gm12878 gse235167 syo-1 chip-seq rna-seq atac-seq

• Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.

  PMID 42203797 · PMC13216315 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated 20 near-complete haplotypes from 10 Japanese male individuals using PacBio HiFi, ONT ultra-long, and Omni-C reads, all with contig N50 exceeding 100 Mbp

  japanese pacbio oxford omni-c

• Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.

  PMID 41252442 · PMC12758600 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

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  Cleanifier is a fast, memory-frugal alignment-free tool for detecting and removing human contamination using gapped k-mers (spaced seeds) and a human pangenome index.

  genomes genome cami t2t host-contamination pangenome

• hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.

  PMID 36498841 · PMC9738810 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 63

  hgtseq is a fully automated, portable, and scalable Nextflow/nf-core pipeline for detecting horizontal gene transfer signatures from unmapped sequencing reads.

  copd chikv bos canis exome taxonomic reference

• Cancer genome standards for long-read sequencing using cancer cell line mixtures.

  PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

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  Long-read variant calling tools achieve recall rates comparable to short-read gold standards

  colo829 same whole-genome short-read 5mc