Reference health
Streamlining data-intensive biology with workflow systems
97/97 checkable references clean · checked 2026-07-14
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a publisher retraction, withdrawal, or removal notice.
42 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 97 checked references that resolve
resolves10.1038/s41587-020-0439-x
The nf-core framework for community-curated bioinformatics pipelines
resolves10.1371/journal.pcbi.1005755
Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
resolves10.1139/facets-2019-0020
A graduate student perspective on overcoming barriers to interacting with open-source software
resolves10.1007/s41019-017-0050-4
Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis
resolves10.1038/s41592-018-0046-7
Bioconda: sustainable and comprehensive software distribution for the life sciences
resolves10.1093/nar/gky379
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
resolves10.1101/737528
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
resolves10.1186/s40168-019-0658-x
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
resolves10.21105/joss.00550
The drake R package: a pipeline toolkit for reproducibility and high-performance computing
resolves10.1016/j.margen.2016.04.012
Next-generation biology: Sequencing and data analysis approaches for non-model organisms
resolves10.1101/2020.07.21.187609
BioContainers Registry: searching for bioinformatics tools, packages and containers
resolves10.1093/gigascience/giy158
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes
resolves10.25080/majora-4af1f417-011
Binder 2.0 - Reproducible, interactive, sharable environments for science at scale
resolves10.1186/s13059-020-02066-4
Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
resolves10.1016/j.future.2017.12.029
Computing environments for reproducibility: Capturing the “Whole Tale”
resolves10.1093/bioinformatics/btz715
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
resolves10.1038/sdata.2016.18
The FAIR Guiding Principles for scientific data management and stewardship
resolves10.1128/AEM.01444-19
Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials
resolves10.1186/s13059-018-1491-4
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
resolves10.1016/j.molp.2018.07.005
FAIR: A Call to Make Published Data More Findable, Accessible, Interoperable, and Reusable
resolves10.1038/sdata.2015.23
Open science resources for the discovery and analysis of Tara Oceans data
resolves10.1093/nar/30.1.207
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
resolves10.1261/rna.058339.116
Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
resolves10.1261/rna.046011.114
Power analysis and sample size estimation for RNA-Seq differential expression
resolves10.1038/nbt.2235
Unlocking the potential of metagenomics through replicated experimental design
resolves10.1016/j.tim.2018.11.003
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
resolves10.1371/journal.pone.0124671
From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
resolves10.1038/nbt.3981
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
resolves10.1038/srep08747
Completing bacterial genome assemblies: strategy and performance comparisons
resolves10.1134/S102279541705012X
Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly
resolves10.1111/mec.14264
Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
resolves10.1111/2041-210X.12700
Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference
resolves10.3389/fgene.2019.00533
Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better?
resolves10.1111/1755-0998.12669
Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations
resolves10.1111/1755-0998.12677
Responsible <scp>RAD</scp>: Striving for best practices in population genomic studies of adaptation
resolves10.1186/s13059-016-0927-y
Design and computational analysis of single-cell RNA-sequencing experiments
resolves10.1186/s13073-017-0467-4
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
resolves10.1093/bib/bbs017
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
resolves10.1038/nmeth.4197
Salmon provides fast and bias-aware quantification of transcript expression
resolves10.1093/bioinformatics/btw354
MultiQC: summarize analysis results for multiple tools and samples in a single report
resolves10.1038/nrg3788
Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
resolves10.1086/BBLv227n2p146
Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters
resolves10.1186/s12864-018-4933-1
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
resolves10.1186/s13059-014-0420-4
Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
resolves10.1073/pnas.1510461112
Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
resolves10.1073/pnas.1600338113
No evidence for extensive horizontal gene transfer in the genome of the tardigrade
<i>Hypsibius dujardini</i>
resolves10.1186/1944-3277-10-18
Large-scale contamination of microbial isolate genomes by Illumina PhiX control
resolves10.1111/1755-0998.13009
Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies
resolves10.1186/s13059-019-1809-x
When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data
resolves10.1038/s41587-019-0201-4
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
resolves10.1093/bioinformatics/btw277
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
resolves10.1007/s10606-018-9333-1
The Types, Roles, and Practices of Documentation in Data Analytics Open Source Software Libraries
resolves10.1371/journal.pcbi.1002216
BioStar: An Online Question & Answer Resource for the Bioinformatics Community
resolves10.1371/journal.pbio.2005561
Building a local community of practice in scientific programming for life scientists
The 42 references without a DOI — listed, not checked
no DOI — not checkedMGnify: the microbiome analysis resource in 2020
no DOI — not checked2024111605594225900_bib17
no DOI — not checked2024111605594225900_bib19
no DOI — not checkedMölder F, Jablonski KP, Letcher B, et al. Sustainable data analysis with Snakemake. Zenodo. 2020. ghdx9x.
no DOI — not checkedCommon Workflow Language, v1.0
no DOI — not checked2024111605594225900_bib27
no DOI — not checkedThe Seven Bridges Platform
no DOI — not checked2024111605594225900_bib127
no DOI — not checked2024111605594225900_bib128
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no DOI — not checkedDocker: lightweight Linux containers for consistent development and deployment
no DOI — not checked2024111605594225900_bib39
no DOI — not checked2024111605594225900_bib41
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no DOI — not checked2024111605594225900_bib57
no DOI — not checked2024111605594225900_bib58
no DOI — not checkedWormBase: a modern Model Organism Information Resource
no DOI — not checkedTen steps to get started in Genome Assembly and Annotation
no DOI — not checked2024111605594225900_bib92
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carried a publisher retraction notice at that time. It says nothing about the quality, findings,
or importance of the work itself, and nothing about references deposited without a DOI.
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