---
title: "MedGenome vs Pepkio: Bioinformatics Service Comparison"
contentType: "ARTICLE"
datePublished: "2026-08-06"
dateModified: "2026-08-06"
canonicalUrl: "/compare/pepkio-vs-medgenome"
---

# MedGenome vs Pepkio: Bioinformatics Service Comparison

The main difference between MedGenome vs Pepkio comes down to whether your project requires integrated wet-lab sequencing with managed summary reports or dedicated dry-lab [RNA-seq analysis](/services/rna-seq) with complete code delivery. Pepkio serves researchers who have raw sequence data (FASTQ, BAM, or count matrices) and need custom executable R or Python scripts, direct analyst communication, publication-ready vector figures, and draft Methods sections. MedGenome provides accredited wet-lab sample processing, library preparation, and high-throughput sequencing alongside dry-lab data processing and clinical variant interpretation via software tools like VarMiner. Dry-lab turnaround for both providers typically ranges from 2 to 4 weeks, with MedGenome extending to 4 to 6 weeks for integrated wet-lab multi-omics projects.

## Quick Comparison Table

| Aspect | Pepkio | MedGenome |
| --- | --- | --- |
| 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 Chromium 3'/5', V(D)J, fixed RNA), spatial transcriptomics (10x Visium), scATAC-seq, scMultiomics, WGS/WES, epigenomics (ChIP-seq, ATAC-seq, WGBS/RRBS), Olink proteomics, mass spectrometry metabolomics |
| Pipeline tools disclosed | Documented open-source tools (STAR, DESeq2, Seurat, GATK) with parameters included in project deliverables | Documented open-source tools (STAR, BWA, DESeq2, CellRanger, GATK) summarized in project reports |
| Code/scripts delivered | Executable R and Python scripts; optional Nextflow or Snakemake workflows and Docker or Conda environments | Processed data tables, BAM/VCF/count matrices, and PDF/HTML summary reports; raw execution scripts are not delivered |
| Reproducibility approach | Complete script handover, parameter logging, version-pinned environments, optional Docker/Conda containers | Managed internal pipeline execution, summary reports, and processed data tables; execution code is not distributed to clients |
| Publication-quality figures | High-resolution editable vector graphics (PDF, SVG) and raster formats (PNG, TIFF) | Visual plots embedded within PDF/HTML reports; raw data tables provided to generate vector plots using external tools |
| Methods-section support | Includes a drafted publication-ready Methods section | Methodological summaries, tool lists, and parameter notes included in summary reports |
| Reviewer-response support | Direct post-delivery analyst support for reviewer questions and re-analyses | Post-delivery technical support consultations; major re-analyses handled via project scope addenda |
| Turnaround time | 2–4 weeks for standard cohorts; 4–6 weeks for complex multi-contrast studies | 2–4 weeks post-QC for dry-lab NGS; 19–21 days for clinical WES; 4–6 weeks for complex wet-lab multi-omics |
| Direct analyst access | Direct contact with lead bioinformaticians executing the analysis | Primary coordination via dedicated project managers; Ph.D. specialists participate in scoping and report review calls |
| Pricing transparency | Fixed project pricing scoped upfront | Custom quotes per sample or project scope |
| Data ownership | 100% client-owned data, code, and intellectual property | Client owns sample data, raw files, and report outputs; internal pipeline code remains MedGenome IP |
| Best suited for | Labs with raw sequence data seeking dry-lab analysis, full code delivery, direct analyst communication, and manuscript support | Labs needing integrated wet-lab extraction, library prep, sequencing under CAP/CLIA accreditation, or clinical variant prioritization |

## What MedGenome Does
MedGenome provides integrated wet-lab sequencing and dry-lab bioinformatics processing across accredited laboratory facilities. Researchers send physical specimens—such as fresh or frozen tissue, FFPE blocks, blood, cell suspensions, or extracted nucleic acids—or transfer raw FASTQ, BAM, and VCF files for standalone dry-lab projects.

Their dry-lab workflows process [bulk RNA-seq](/services/rna-seq) (differential expression, alternative splicing, and pathway enrichment), [single-cell transcriptomics](/services/single-cell) (10x Chromium 3' and 5' gene expression, TCR/BCR V(D)J profiling, and scATAC-seq), [spatial transcriptomics](/services/spatial-transcriptomics) (10x Visium), WGS and [variant calling](/services/variant-calling), epigenomics ([ChIP-seq](/services/chip-seq), ATAC-seq, WGBS), targeted Olink proteomics, and mass spectrometry metabolomics.

Pipelines use standard open-source tools including STAR, BWA, Bowtie2, featureCounts, DESeq2, edgeR, CellRanger, Seurat, and GATK, alongside proprietary software such as VarMiner for clinical variant prioritization and DISQVER for metagenomic pathogen detection. Deliverables include raw FASTQ files via S3 or cloud links, aligned BAM files, annotated VCFs, gene count matrices, single-cell object files (h5ad, Seurat RDS), and PDF/HTML summary reports containing QC summaries and differential expression tables.

## What Pepkio Does
Pepkio provides dedicated dry-lab bioinformatics analysis for researchers who already have raw sequencing data. Researchers transfer FASTQ files, BAM alignments, or count matrices, which Pepkio's bioinformaticians process across [bulk RNA-seq](/services/rna-seq), [single-cell pipelines](/services/single-cell), [spatial transcriptomics](/services/spatial-transcriptomics) (10x Visium/Visium HD), WGS/WES [variant calling](/services/variant-calling), [ChIP-seq](/services/chip-seq), ATAC-seq, metagenomics, and [proteomics](/services/proteomics).

Workflows run standard open-source tools including STAR, fastp, DESeq2, Seurat, and GATK. Pepkio delivers executable R and Python scripts, normalized count matrices, differential expression tables, publication-ready vector graphics (PDF/SVG), optional Nextflow or Snakemake workflows, optional Docker or Conda environments, and a draft Methods section written for manuscript submission.

Projects follow a direct support model where researchers work directly with the computational biologist executing their dataset. This direct contact covers pre-project scoping, parameter adjustments during analysis, and post-delivery support for addressing reviewer comments during peer review.

## MedGenome vs Pepkio: Feature Comparison

### Analysis scope & organism support
MedGenome supports human, mouse, rat, non-human primates, agricultural crops, microbes, and non-model organisms. Because MedGenome operates physical sequencing instruments (Illumina NovaSeq X Plus, NovaSeq 6000, NextSeq, Oxford Nanopore, 10x Chromium X, Olink Signature Q100), they handle physical tissue extraction and specialized wet-lab assays such as WGBS/RRBS methylation, Olink targeted proteomics, and mass spectrometry metabolomics. Pepkio focuses strictly on dry-lab computational workflows from submitted data files, supporting bulk and single-cell RNA-seq, spatial transcriptomics, WGS/WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics across model and non-model organisms.

### Pipeline transparency and tool documentation
Pepkio provides complete script files and parameter logs detailing exact filtering cutoffs, normalization logic, and statistical settings. MedGenome lists tool names (such as STAR, BWA, DESeq2, and GATK) and parameter choices inside final PDF/HTML summary reports, operating as a managed service where raw execution scripts remain internal.

### Reproducibility & code delivery
Pepkio hands over executable R and Python scripts along with version-pinned environment files, with optional Nextflow or Snakemake workflows and Docker or Conda containers. Researchers can inspect, modify, or rerun the code on their own computational infrastructure. MedGenome provides processed data files (BAM, VCF, count matrices, h5ad/RDS files) and PDF/HTML summary reports, but does not distribute executable script files, workflow manager definitions, or container images to clients.

### Publication support (figures, Methods text, reviewer responses)
Pepkio delivers publication-ready vector graphics (PDF, SVG), writes a complete draft Methods section covering pipeline steps and parameters, and provides direct analyst support to answer journal reviewer questions or perform requested re-analyses. MedGenome embeds visual plots within PDF/HTML reports and provides raw data tables so researchers can generate vector graphics independently; they supply methodological text summaries in reports and offer post-delivery technical consultations, with major re-analyses handled via scope updates.

### Turnaround & deadline flexibility
Pepkio completes dry-lab analyses in 2 to 4 weeks for standard datasets and 4 to 6 weeks for complex multi-contrast studies. MedGenome's turnaround ranges from 2 to 4 weeks for dry-lab NGS post-QC, 19 to 21 working days for clinical WES panels, and 4 to 6 weeks for complex wet-lab multi-omics projects from sample arrival to final report delivery.

### Communication model (analyst access vs. project-manager relay)
Pepkio pairs researchers directly with the lead bioinformatician handling their data via email, video calls, or direct messaging channels. MedGenome routes day-to-day project tracking and administrative communications through dedicated project managers, with Ph.D. bioinformatics specialists participating in initial scoping calls and post-report review meetings.

### Pricing & what's included
Neither service posts static price tables online; both issue custom quotes after project scoping. MedGenome quotes pricing per sample or project, with standard packages covering primary processing, reports, cloud transfer, standard data storage (30 days to 6 months), and initial technical consultations. Pepkio provides fixed-price project quotes scoped upfront, covering data processing, code handover, vector figure generation, Methods text drafting, and reviewer response support.

### Data handling & security
MedGenome retains project data for 30 days to 6 months post-delivery (with extended cloud storage available for an extra fee) and operates CAP-accredited and CLIA-certified laboratory facilities. Pepkio transfers final deliverables, scripts, and processed data upon project completion, granting researchers 100% ownership of code, data, and intellectual property.

### Handling non-standard or custom analyses
Pepkio customizes R and Python scripts during scoping to handle custom experimental designs, non-standard reference genomes, or specialized statistical logic, delivering all modified code upon completion. MedGenome handles custom analytical requests or non-standard protocols through project scope addenda and provides specialized clinical variant prioritization using proprietary software like VarMiner.

## When Pepkio Is the Better Fit
- You already have raw FASTQ, BAM, or count files and need dedicated dry-lab analysis.
- You require raw, executable R or Python scripts to inspect parameters, adjust plot styles, or maintain local computational reproducibility.
- You want direct, ongoing communication with the bioinformatician executing your code.
- You need manuscript-ready vector figures (SVG/PDF) and a fully drafted Methods section for publication.
- You prefer fixed-scope project pricing upfront without fee addenda for script delivery.

## When MedGenome Is the Better Fit
- You need a single service provider to handle physical tissue extraction, library preparation, high-throughput sequencing, and bioinformatics under one contract.
- Your project requires accredited wet-lab processing under CAP accreditation or CLIA certification.
- You require specialized wet-lab assays such as WGBS methylation, Olink targeted proteomics, or mass spectrometry metabolomics.
- Your clinical research benefits from proprietary variant prioritization tools such as VarMiner and pathogen detection platforms like DISQVER.
- You prefer a managed service report model (PDF/HTML) where pipeline execution is handled entirely by the CRO.

## Trade-Offs at a Glance

| Factor | Pepkio | MedGenome |
| --- | --- | --- |
| Wet-lab sequencing | Requires existing digital data files | Integrated CAP/CLIA wet-lab facilities & dry-lab pipelines |
| Script & code deliverables | Executable R/Python scripts; optional Nextflow/Docker | Managed pipelines; summary reports & data tables delivered |
| Communication structure | Direct contact with lead bioinformatician | Dedicated project manager relay with Ph.D. review calls |
| Regulatory certifications | Dry-lab computational focus | CAP-accredited, CLIA-certified laboratory facilities |
| Turnaround options | Standard 2–4 week dry-lab delivery | 2–4 weeks dry-lab; 19–21 days clinical WES; 4–6 weeks wet-lab |

## Frequently Asked Questions

### Do I get the actual R or Python scripts used to analyze my data?
Pepkio delivers complete executable R and Python scripts, parameter logs, and optional Docker or Conda environment configurations so your team can inspect or rerun the workflow locally. MedGenome operates a managed service model that provides processed data tables, alignment files, and PDF/HTML summary reports, but does not distribute internal execution scripts or pipeline source code.

### Can MedGenome handle both wet-lab sequencing and dry-lab bioinformatics?
Yes. MedGenome operates CAP-accredited and CLIA-certified laboratory facilities, providing end-to-end processing from physical tissue, blood, or FFPE samples through library prep, sequencing on platforms like Illumina NovaSeq X Plus, and downstream bioinformatics reporting. Pepkio focuses strictly on dry-lab bioinformatics analysis for researchers who already have raw data files.

### Who do I talk to when I have questions about my data analysis?
With Pepkio, you communicate directly with the lead bioinformatician executing your code via email, video calls, or direct channels throughout the project. With MedGenome, day-to-day updates and project logistics are managed by dedicated project managers, while Ph.D. bioinformatics specialists participate in pre-project scoping calls and post-report review sessions.

### Will either service draft the Methods section for my manuscript?
Pepkio includes a draft publication-ready Methods section detailing reference genomes, alignment parameters, statistical cutoffs, and software packages used. MedGenome provides methodological summaries, software tool lists, and parameter notes within the final project report, which researchers can adapt into their manuscript Methods section.

### How do both providers handle journal Reviewer 2 comments during peer review?
Pepkio provides direct analyst support during peer review to address reviewer questions, explain parameter choices, or run requested statistical re-analyses. MedGenome provides post-delivery technical support consultations to answer methodology questions; requests for major re-analyses or new computational workflows driven by peer review are evaluated case-by-case and handled via project scope addenda.

### What data files do I receive at the end of a project?
MedGenome delivers raw FASTQ files via S3 or cloud links, aligned BAM/CRAM files, annotated VCFs, gene count matrices, single-cell object files (h5ad or Seurat RDS), and PDF/HTML summary reports. Pepkio delivers standard data files alongside raw executable R/Python scripts, normalized matrices, publication-ready vector graphics (PDF/SVG), and optional Nextflow or Snakemake workflows.

### Can I send existing FASTQ files if I already completed sequencing elsewhere?
Yes, both providers accept existing digital data. MedGenome accepts raw FASTQ, BAM, VCF, and count matrix files for standalone dry-lab re-analysis. Pepkio operates as a dedicated dry-lab service processing submitted FASTQ files, alignment files, and count matrices.

### How long does the analysis take from submission to final delivery?
Pepkio completes dry-lab bioinformatics projects in 2 to 4 weeks for standard cohorts and 4 to 6 weeks for complex multi-contrast studies. MedGenome's turnaround ranges from 2 to 4 weeks for dry-lab NGS post-QC, 19 to 21 working days for clinical WES panels, and 4 to 6 weeks for complex integrated wet-lab multi-omics projects from sample arrival.

### Who owns the computational scripts and analysis output?
Pepkio grants clients 100% ownership of all delivered R/Python scripts, data files, figures, and intellectual property. MedGenome clients own their physical sample data, raw sequencing data, and final analytical output tables and reports, while MedGenome retains ownership of its internal pipeline code and proprietary software such as VarMiner.

### What happens to my data after the project ends?
MedGenome retains project data for 30 days to 6 months post-delivery under standard contract terms, with extended cloud storage options available for an extra fee. Pepkio transfers all final deliverables and project files directly to the client upon project completion.

### How is pricing structured, and are there public price lists?
Neither provider lists static pricing on public web pages; both issue custom project quotes after scoping. MedGenome quotes per sample or per project scope based on wet-lab and dry-lab requirements. Pepkio provides fixed-price project quotes scoped upfront based on dataset complexity and analytical goals.

### Can either service handle non-model organisms or non-standard experimental designs?
Yes. MedGenome supports non-model and custom reference organisms across sequencing and bioinformatics applications. Pepkio customizes R and Python scripts during initial scoping to accommodate custom reference assemblies, non-standard experimental designs, and custom statistical logic, delivering all modified code upon completion.

## Bottom Line
Choosing between MedGenome vs Pepkio comes down to your project's starting point and computational requirements. If you need physical sample extraction, high-throughput sequencing under CAP/CLIA accreditation, or specialized wet-lab multi-omics like Olink proteomics, MedGenome provides an integrated wet-lab and dry-lab solution with managed PDF/HTML reports. If you already have raw data files and want a dedicated dry-lab service that delivers executable R/Python scripts, publication-ready vector figures, a drafted Methods section, and direct communication with the bioinformatician handling your data, Pepkio provides the open computational workflow your research requires.


:::disclaimer
This comparison is based on publicly available information at the time of writing. Services, pricing, and policies may change over time; please verify the latest details directly with the relevant provider.
:::

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