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).

• De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.

  PMID 34072576 · PMC8227486 · Genes · 2021 · 7 claims · 8 setups

  Has reproduction · 87

  A new consensus transcriptome of E. gracilis was assembled by combining reads from five independent RNA-seq studies (23 samples)

  euglena gracilis consensus bulk in-house novo

• Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

  PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

  Has reproduction · 91

  SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

  deep co-assembled surf_17 surf_5 whole-genome novo 16s

• Whole genome amplification and de novo assembly of single bacterial cells.

  PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

  prochlorococcus single-cell seven sag genome spike-in amplification

• metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

  PMID 41530917 · PMC12818822 · Gut microbes · 2026 · 8 claims · 8 setups

  Full-text index only

  metaFun is an open-source, end-to-end Nextflow/Apptainer pipeline integrating quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomics, network analysis, and strain-level microdiversity analysis into a unified framework

  simulated selected gut mags novo binning pangenome-based

• A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

  PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups

  Has reproduction · 75

  Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.

  pure enriched stec-negative extracted ont real-time artificial

• A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.

  PMID 24809511 · PMC4014436 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  The Helicosporidium nuclear genome is small and compact (~2.5-fold smaller than Chlorella and Coccomyxa) yet shows almost no evidence of functional/metabolic reduction.

  helicosporidium ten whole-genome transcriptome gene

• Assembling unmapped reads reveals hidden variation in South Asian genomes.

  PMID 41963335 · PMC13246962 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Conventional mapping-based approaches systematically overlook genetic variation in regions that differ substantially from the reference genome

  1kgp unmapped assembled sas short-read novo contamination

• A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis.

  PMID 40323688 · PMC12584591 · The Journal of heredity · 2025 · 6 claims · 8 setups

  Has reproduction · 99

  This paper presents the first de novo, haplotype-resolved reference-quality genome assembly of Sebastes paucispinis (bocaccio rockfish).

  sebastes assembled pacbio omni-c k-mer

• nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.

  PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.

  simulated assembled mags raw metagenomic novo genome

• Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis.

  PMID 42224013 · PMC13225438 · Microbial genomics · 2026 · 8 claims · 6 setups

  Full-text index only

  The H37Rv_ref reference genome, sequenced in 1998 with early technology, is incomplete relative to modern hybrid-sequenced assemblies

  tuberculosis h37rv_cn a2018772 publicly hybrid comparative functional

• Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

  PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

  six same polished each nanopore illumina novo

• First genome assemblies of Neotropical Thoracobombus bumblebees Bombus pauloensis and Bombus pullatus.

  PMID 41436027 · PMC12958814 · G3 (Bethesda, Md.) · 2026 · 7 claims · 8 setups

  Full-text index only

  This study produced the first genome assemblies of Neotropical Bombus (Thoracobombus) species, B. pauloensis and B. pullatus

  pauloensis masked long-read k-mer novo

• The Nuclear and Mitochondrial Genomes of the Lined Rockskipper, Istiblennius lineatus (Teleostei: Blenniidae).

  PMID 42117780 · PMC13195801 · Genome biology and evolution · 2026 · 7 claims · 8 setups

  Full-text index only

  A chromosome-scale nuclear genome assembly of I. lineatus (643.23 Mb, 24 pseudochromosomes) was generated using PacBio HiFi reads and Arima Hi-C scaffolding.

  istiblennius lineatus pacbio hi-c rna-seq

• Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.

  PMID 31346012 · PMC6658682 · Microbiology resource announcements · 2019 · 6 claims · 7 setups

  Has reproduction · 92

  Draft genome sequences of three multidrug-resistant Shigella clinical isolates from Pakistan (two S. flexneri, one S. sonnei) are reported as a resource for AMR surveillance.

  shigella bacterial antimicrobial whole-genome

• The genome sequence of the Spanish Festoon, Zerynthia rumina (Linnaeus, 1758) (Lepidoptera: Papilionidae).

  PMID 41769331 · PMC12946699 · Wellcome open research · 2026 · 8 claims · 7 setups

  Full-text index only

  A genome assembly for Zerynthia rumina was produced, containing two haplotypes of 852.84 Mb and 775.60 Mb

  organism genomic assembled haplotype pacbio hi-c k-mer

• The genome sequence of the Lesser Horseshoe Bat, Rhinolophus hipposideros (Bechstein, 1800) (Chiroptera: Rhinolophidae).

  PMID 42004187 · PMC13090764 · Wellcome open research · 2026 · 8 claims · 6 setups

  Full-text index only

  A phased, chromosome-level genome assembly was produced for Rhinolophus hipposideros as part of the Bat1K and Darwin Tree of Life projects.

  rhinolophus pacbio hi-c sequencing

• The genome sequence of the nematode Ostertagia ostertagi (Stiles, 1892) (Rhabditida, Trichostrongylidae).

  PMID 42094077 · PMC13139848 · Wellcome open research · 2026 · 8 claims · 7 setups

  Full-text index only

  A chromosome-level genome assembly was generated for a single male specimen of Ostertagia ostertagi (isolate MOo2).

  single pooled unassembled assembled pacbio hi-c k-mer

• DFAST and DAGA: web-based integrated genome annotation tools and resources.

  PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups

  Has reproduction · 89

  DFAST is a web-based genome annotation pipeline with integrated quality assessment (CheckM) and taxonomic assessment (ANI) that produces DDBJ submission-ready files

  lactobacillus representative lab genomes genome average novo

• MoGAAAP: a modular Snakemake workflow for automated genome assembly and annotation with quality assessment.

  PMID 41585413 · PMC12824462 · NAR genomics and bioinformatics · 2026 · 8 claims · 8 setups

  Full-text index only

  MoGAAAP is a modular Snakemake pipeline that automates assembly, provisional annotation, and quality assessment (QA) for any diploid eukaryotic organism

  arabidopsis grapevine pangenome invertebrate genome novo gene

• Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

  PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

  Has reproduction · 83

  MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

  pooled hc227 contig sets shotgun novo alignment-free