Fios Genomics vs Pepkio: Bioinformatics Service Comparison
The main difference between Pepkio and Fios Genomics comes down to whether your lab requires executable script handover for local execution or password-protected interactive web reports paired with scheduled teleconferences. In this Pepkio vs Fios Genomics comparison, both providers operate as dry-lab computational biology contract research organizations (CROs) that analyze raw sequencing data without running physical wet labs. Pepkio provides raw R and Python scripts, optional Docker or Conda environments, optional Nextflow or Snakemake workflows, and direct ongoing access to the lead bioinformatician. Fios Genomics delivers password-protected interactive HTML reports with filterable figures, structured summaries, and scheduled video walkthroughs with their lead analyst. Standard [RNA-seq analysis](/services/rna-seq) projects with Pepkio take 2 to 4 weeks with full script ownership. Fios Genomics offers fixed-cost packages like FGEz for standard projects alongside customized multi-omics proposals.
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Quick Comparison Table
| Aspect | Pepkio | Fios Genomics |
|---|---|---|
| Analysis types supported | Bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics (10x Visium/Visium HD), WGS/WES variant calling, ChIP-seq, ATAC-seq, metagenomics, proteomics | Bulk RNA-seq, scRNA-seq (10x, DropSeq, Parse, SMART-Seq2), spatial transcriptomics (10x, NanoString, Vizgen), WGS/WES, GWAS, epigenomics, LC-MS/MS & Olink proteomics, metabolomics, multi-omics integration |
| Pipeline tools & versions disclosed | Documented tools (STAR, fastp, DESeq2, Seurat, GATK) with versions and parameters included in project deliverables | Documented tools (STAR, BWA, DESeq2, Limma, Seurat, Scanpy, GATK) with versions detailed in final report Methods sections |
| Code/scripts delivered | Executable R and Python scripts; optional Nextflow/Snakemake workflows and Docker/Conda containers | Interactive HTML reports, static PDFs, summary tables, and processed data matrices; raw executable scripts are not standard deliverables |
| Reproducibility approach | Executable script handover, parameter logging, and optional containerized or workflow execution environments | Interactive HTML reporting, structured processed tables, and documented Methods text |
| Publication-quality figures | High-resolution editable vector graphics (PDF, SVG) and raster formats (PNG, TIFF) | Interactive web visualisations (volcano plots, UMAPs, heatmaps) and downloadable vector (SVG, PDF) and PNG static figures |
| Methods-section support | Drafted publication-ready Methods section detailing tools, parameters, and references | Dedicated publication-ready Methods section embedded directly inside the interactive HTML report |
| Reviewer-response support | Direct technical support with the lead bioinformatician for reviewer queries and re-analyses | Post-report follow-up support for peer-reviewer questions, methods clarification, and supplementary explanations |
| Turnaround time | 2–4 weeks for standard cohorts; 4–6 weeks for complex multi-contrast studies | Standardized timelines for single-datatype studies (FGEz); custom timelines set during scoping for complex studies |
| Direct analyst access | Direct ongoing contact with lead bioinformaticians via email and video calls | Scheduled post-analysis video teleconference with the lead bioinformatician, alongside scoping and project management contact |
| Pricing transparency | Quote-based fixed project pricing scoped upfront per study | Quote-only fixed-cost packages (including FGEz) and FTE/retainer models based on project consultation |
| Data ownership | 100% client-owned data, custom scripts, and IP | 100% client-owned data and IP; internal pipeline codebase retained by vendor |
| Best suited for | Labs with raw data seeking dry-lab analysis, executable script handover, direct analyst access, and manuscript support | Researchers needing interactive web reports for non-coders, post-analysis video review, and multi-omics or clinical data integration |
What Fios Genomics Does
Fios Genomics operates as a dry-lab computational biology CRO, accepting raw data files without running an in-house wet lab or physical sequencers. Researchers send raw FASTQ files, BAM alignments, VCF variant files, count matrices, microarrays, Olink protein quantifications, or mass spectrometry tables.
Fios Genomics provides dry-lab analysis across bulk RNA-seq, single-cell RNA-seq (10x Genomics, DropSeq, Parse Biosciences, SMART-Seq2), spatial transcriptomics (10x Visium/Xenium, NanoString GeoMx/CosMx, Vizgen MERSCOPE), WGS/WES, GWAS, epigenomics, LC-MS/MS proteomics, metabolomics, lipidomics, and multi-omics integration. Established open-source tools in their workflows include edgeR, limma, DESeq2, STAR, Bowtie, BWA, CellRanger, Seurat, Scanpy, GATK, and WGCNA. Supported organisms include human, mouse, rat, livestock, aquaculture species such as gilthead sea bream, plants, and microbial communities.
Deliverables consist of password-protected interactive HTML reports with searchable tables, filterable plots, and embedded Methods text, alongside downloadable static PDF, SVG, and PNG figures. Each project includes a scheduled video teleconference with the lead bioinformatician to review findings and discuss biological interpretation. The service caters to academic, biotech, and biopharma teams seeking dry-lab data interpretation without writing code.
What Pepkio Does
Pepkio provides dry-lab bioinformatics analysis for research teams with raw sequencing or omics datasets. Analysis modalities cover bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics (10x Visium/Visium HD), WGS/WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics.
Pipelines incorporate standard open-source tools such as STAR, fastp, DESeq2, Seurat, and GATK. Pepkio delivers raw, executable R and Python scripts, parameter logs, normalized matrices, differential analysis tables, editable vector figures (PDF/SVG), and a draft Methods section. Workflows can optionally be delivered as Nextflow or Snakemake pipelines and packaged in Docker or Conda environments.
Researchers communicate directly with the senior computational biologist executing their project. This access spans initial scoping, parameter adjustments during analysis, and post-delivery technical support to address reviewer comments.
Pepkio vs Fios Genomics: Head-to-Head Comparison
Which analyses and organisms are supported?
Both providers analyze data from human, rodent, plant, microbial, livestock, and non-model species. Fios Genomics offers broader multi-omics options, including LC-MS/MS metabolomics, lipidomics, Olink protein panels, GWAS, and joint statistical integration with clinical metadata. Pepkio focuses on core NGS and omics modalities: bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, WGS/WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics.
How transparent and reproducible are the pipelines?
Pepkio hands over full, executable R and Python scripts, exact parameter settings, and statistical filtering cutoffs. Workflow execution can optionally be delivered via Nextflow or Snakemake, and packaged in Docker or Conda containers for local execution. Fios Genomics documents software names, statistical models, and database references in the Methods section of final reports, but retains executable pipeline code within its internal codebase.
What publication and reviewer support is included?
Both services provide manuscript preparation assistance. Pepkio delivers editable vector figures (SVG, PDF), a draft Methods section, and direct support from the assigned bioinformatician to perform re-analyses for reviewer queries. Fios Genomics delivers interactive web visualisations, static SVG/PDF vector figures, an embedded Methods section, and post-report technical support for peer-review questions.
What are turnaround times and communication workflows?
Pepkio completes standard cohort studies in 2 to 4 weeks, and complex multi-contrast projects in 4 to 6 weeks. Researchers work directly with their assigned senior computational biologist via email and calls throughout execution. Fios Genomics provides rapid delivery for standardized single-datatype studies (FGEz) and custom timelines for complex projects, concluding with a scheduled post-analysis video conference with the lead analyst.
How do pricing and licensing models compare?
Neither provider publishes fixed online price lists; both provide custom quotes following scoping discussions. Pepkio uses study-based fixed quotes covering data processing, executable script handover, vector figures, Methods text, and reviewer support. Fios Genomics offers fixed-cost packages alongside FTE retainer arrangements for enterprise biopharma collaborations, with clients owning their data while Fios retains its internal codebase.
When Pepkio Is the Better Fit
- You need raw, executable R or Python scripts for local execution, inspection, or customization.
- You require optional containerized environments (Docker/Conda) or workflow manager scripts (Nextflow/Snakemake) to integrate with internal infrastructure.
- You want direct ongoing communication with the bioinformatician analyzing your dataset throughout execution.
- You need editable vector graphics (SVG/PDF), a draft Methods section, and direct analyst assistance during peer review.
- You prefer fixed-price scoping per study with complete code handover.
When Fios Genomics Is the Better Fit
- You prefer password-protected interactive HTML reports that allow team members without programming experience to filter and explore data.
- Your project requires multi-omics integration across transcriptomics, LC-MS/MS proteomics, metabolomics, lipidomics, and clinical metadata.
- You value a structured post-analysis video teleconference with the lead bioinformatician to discuss biological interpretation.
- You require ongoing Full-Time Equivalent (FTE) or retainer arrangements for enterprise or multi-project research.
- You are analyzing niche sample types or agricultural/aquaculture species such as gilthead sea bream (Sparus aurata).
Trade-Offs at a Glance
| Factor | Pepkio | Fios Genomics |
|---|---|---|
| Code deliverable | Executable R/Python scripts (optional Nextflow/Snakemake, Docker/Conda) | Interactive HTML reports and processed data tables |
| Primary communication | Direct ongoing access to lead bioinformatician | Scheduled post-analysis video consultation |
| Data exploration | Script modification and editable vector figures | Password-protected web-based interactive HTML reports |
| Commercial model | Fixed-scope project pricing | Fixed-cost packages (FGEz) and FTE/retainers |
| Multi-omics scope | Core NGS, single-cell, spatial, variant calling, ChIP/ATAC, proteomics | Multi-omics, LC-MS/MS, Olink, metabolomics, lipidomics, clinical data |
Frequently Asked Questions
Do I get the actual R or Python scripts used to analyze my data?
Pepkio delivers executable R and Python scripts, parameter logs, and optional Docker/Conda or Nextflow/Snakemake environments for local reruns. Fios Genomics delivers interactive HTML reports and processed data tables, retaining internal pipeline code within its internal codebase.
How do interactive web reports compare to receiving code files?
Interactive HTML reports from Fios Genomics allow researchers to search data tables, filter plots, and inspect results in a web browser without writing code. Receiving raw executable script files from Pepkio allows computational team members to modify statistical cutoffs, customize visualizations in R or Python, and execute pipelines on local hardware.
Will either team write the Methods section for my manuscript?
Pepkio includes a draft publication-ready Methods section detailing reference assemblies, alignment tools, statistical thresholds, and software packages used. Fios Genomics embeds a dedicated, publication-ready Methods section directly inside their interactive HTML report, covering software packages, statistical models, and references.
How do both providers handle journal Reviewer 2 comments during peer review?
Pepkio provides direct post-delivery support where the bioinformatician who executed your analysis helps answer reviewer questions, adjust figures, or perform requested re-analyses. Fios Genomics provides post-report follow-up support to assist clients in answering reviewer questions, clarifying methods, or supplying supplementary explanations during peer review.
Do both providers accept raw data from any sequencing platform?
Yes. Both operate as dry-lab CROs that process raw FASTQ, BAM, VCF, and count matrix files generated across Illumina, Oxford Nanopore, PacBio, or array platforms.
Do I talk directly to the bioinformatician working on my project?
With Pepkio, you communicate directly with the senior computational biologist performing your analysis throughout the project via email or video calls. Fios Genomics includes a scheduled post-analysis video teleconference directly with the lead bioinformatician who conducted the analysis to review findings and discuss biological interpretation.
What file formats do I receive for publication figures?
Pepkio supplies publication-ready figures in editable vector formats (SVG, PDF) as well as high-resolution raster files (PNG, TIFF). Fios Genomics provides interactive web visualisations in their HTML reports and downloadable publication-grade static figures in vector (SVG, PDF) and PNG formats.
What is the typical turnaround time for a bioinformatics project?
Pepkio typically completes standard bulk RNA-seq cohort analyses in 2 to 4 weeks from data receipt, extending to 4 to 6 weeks for multi-contrast studies. Fios Genomics emphasizes rapid turnaround using FGEz for standardized single-datatype studies, with timelines for complex multi-omics projects established during initial scoping.
Are prices listed publicly on their websites?
Neither Pepkio nor Fios Genomics publishes static price tables on public web pages. Both generate custom quotes based on sample numbers, experimental design, and analytical scope following an initial consultation.
Who owns the resulting code, processed data, and intellectual property?
Under both options, researchers retain 100% ownership of their data, results, and intellectual property. Pepkio also transfers complete ownership of custom R and Python scripts written for the project, whereas Fios Genomics retains ownership of its internal proprietary codebase.
Can either provider handle non-model organisms or unusual sample types?
Yes. Both accept datasets from non-model plants, animals, and microbial communities. Fios Genomics specifically documents work with agricultural species, aquaculture (sea bream), wildlife vectors, and FFPE tissues alongside human and rodent samples.
What happens if I need long-term bioinformatics consulting instead of a single project?
Fios Genomics offers Full-Time Equivalent (FTE) and retainer models for ongoing biopharma collaborations and exploratory research. Pepkio provides fixed-price project quotes scoped per study, with options to scope follow-up phases as additional project agreements.
Bottom Line
Choosing between Pepkio and Fios Genomics depends on whether your lab requires executable script handover for local reruns or web-based interactive reporting paired with analyst consultations. Pepkio suits research teams seeking complete code transparency, executable R/Python scripts, optional containerized environments, direct analyst communication, and manuscript support. Fios Genomics fits teams looking for browser-based data exploration, interactive HTML reports, scheduled post-analysis video walkthroughs, and broad multi-omics or clinical data integration.
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