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 · 90
An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.
PMID 36891809 · PMC10151396 · G3 (Bethesda, Md.) · 2023 · 8 claims · 8 setups
Combining ONT long reads with Bionano optical maps produced a substantially more complete and contiguous pearl millet Tift 23D2B1-P1-P5 assembly than the prior short-read assembly.
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Has reproduction · 90
Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).
PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups
Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.
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More biology from the sequence.
PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups
The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.
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An analysis of the feasibility of short read sequencing.
PMID 16275781 · PMC1278949 · Nucleic acids research · 2005 · 8 claims · 8 setups
Re-sequencing and de novo sequencing of the majority of a bacterial genome is possible with read lengths of 20-30 nt.
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Has reproduction · 80
Structure of the intergenic spacers in chicken ribosomal DNA.
PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups
Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.
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Has reproduction · 58
HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.
PMID 26945881 · PMC4779561 · BMC genomics · 2016 · 8 claims · 7 setups
HGA leads to significant improvement in assembly quality (N50 and corrected N50) for all 7 evaluated GAGE-B bacterial datasets using most of the 8 evaluated assemblers
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Has reproduction · 100
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
nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.
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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
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Has reproduction · 95
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups
transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms
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Has reproduction · 45
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups
Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Metagenomic analysis of human diarrhea: viral detection and discovery.
PMID 18398449 · PMC2290972 · PLoS pathogens · 2008 · 8 claims · 7 setups
Micro-mass sequencing (minimal stool input, minimal purification, ~384 reads/sample) can detect known enteric viruses in diarrhea specimens
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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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Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.
PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups
The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation
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Has reproduction · 83
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.
PMID 37129547 · PMC10191607 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 1 setups
VirPipe is a new bioinformatics pipeline for detecting viral genomes from Nanopore or Illumina sequencing input with streamlined installation and customization.
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Has reproduction · 99
A chromosome-level genome assembly of Plantago ovata.
PMID 36707685 · PMC9883528 · Scientific reports · 2023 · 8 claims · 8 setups
A chromosome-level reference genome assembly of P. ovata was constructed using PacBio long reads and Hi-C scaffolding.
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Has reproduction · 49
Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing.
PMID 36895650 · PMC9988679 · iScience · 2023 · 8 claims · 8 setups
C. agrestis and K. uniflora are sister species with contrasting reproductive modes, providing a natural system to test effects of sexual vs asexual reproduction on genome evolution
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Has reproduction · 73
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.
PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups
De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp
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Has reproduction · 76
What the Phage: a scalable workflow for the identification and analysis of phage sequences.
PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups
WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.