Eurofins Genomics vs Pepkio: Bioinformatics Service Comparison
The practical difference between Pepkio and Eurofins Genomics is whether you need wet-lab sequencing with standardized reports or a dry-lab partner that returns executable source code. Eurofins Genomics handles physical sample preparation, NGS sequencing, and HTML/PDF summary reports in 10 to 20 business days, and keeps raw computational workflows in house. Pepkio works on existing FASTQ, BAM, or count data and delivers executable R and Python scripts, editable vector figures, and direct access to a computational biologist in 2 to 4 weeks. Send samples to Eurofins Genomics when you need sequencing plus automated reporting. Choose Pepkio when you already have sequencing data and want script handover, analyst collaboration, and peer-reviewer support.
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Quick Comparison Table
| Aspect | Pepkio | Eurofins 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 (INVIEW Transcriptome), scRNA-seq, human WGS, non-human resequencing, WES, ChIP-seq, WGBS (INVIEW Epigenome), Olink & SOMAmer proteomics, microbiome (16S/18S/ITS), shotgun metagenomics |
| Pipeline tools & parameters disclosed | Standard open-source tools (STAR, DESeq2, Seurat, GATK, MACS2) with exact software versions documented in project deliverables | Standard open-source tools (STAR, HISAT2, DESeq2, edgeR, GATK, QIIME2, MACS2) with software versions documented in delivered project reports |
| Code/scripts delivered | Executable R and Python scripts; optional Nextflow or Snakemake workflows and optional Docker or Conda containers | Summary execution reports (HTML/PDF), processed data tables, BAM/VCF files, and FASTQ downloads; raw execution scripts are not delivered |
| Reproducibility approach | Executable script handover, parameter logs, version-pinned environment files, and optional Docker or Conda containers | Managed BioIT workflows, summary PDF/HTML execution reports, and processed data matrices; source code and workflow files are not distributed |
| Publication-quality figures | High-resolution editable vector graphics (PDF, SVG) and raster formats (PNG, TIFF) | High-resolution static report figures (heatmaps, volcano plots, PCA) in raster (PNG) and vector (PDF, SVG) formats |
| Methods-section support | Drafted publication-ready Methods section detailing tools, parameter settings, and reference builds | Structured methodology descriptions, tool citations, and parameter notes embedded in final analysis reports |
| Reviewer-response support | Direct technical support from the lead bioinformatician for peer-reviewer queries and re-analyses | Technical support to clarify pipeline parameters; formal written responses or free re-analyses handled separately |
| Turnaround time | 2–4 weeks for standard cohorts; 4–6 weeks for complex multi-contrast studies | 1–2 days for plasmids/Sanger; 2–5 days for bacterial WGS/amplicons; 10–14 days for clinical WGS/microbiome; 10–20 days for standard NGS |
| Direct analyst access | Direct contact with the lead computational biologist executing the analysis via email and video calls | Primary communication routed through an assigned Project Manager; technical consultation calls arranged during scoping |
| Pricing transparency | Fixed-price project quotes scoped upfront with no speed surcharges | Quote-based pricing per sample or project for NGS and custom BioIT; volume-based options available |
| Data ownership | 100% client-owned data, custom scripts, figures, and IP | 100% client-owned raw sequencing data and derived analytical tables/reports; internal pipeline software remains proprietary |
| Best suited for | Labs with raw data needing dry-lab analysis, executable script handover, direct analyst access, and reviewer support | Labs requiring integrated wet-lab sequencing, certified laboratory infrastructure, high-throughput runs, or Olink proteomics |
What Eurofins Genomics Does
Eurofins Genomics combines high-throughput sequencing infrastructure with standardized dry-lab bioinformatics processing. Laboratories send physical samples, including isolated DNA/RNA, whole blood, fresh or frozen tissues, FFPE blocks, cell lines, or microbial cultures, for library preparation and sequencing on Illumina (NovaSeq X Plus, NovaSeq 6000), Oxford Nanopore (GridION, PromethION), or MGI (DNBSEQ-T7) instruments.
Their analysis catalog covers eukaryotic strand-specific bulk RNA-seq (INVIEW Transcriptome), prokaryotic total RNA-seq, single-cell RNA-seq (scRNA-seq for ready-to-load libraries), Human Whole Genome Sequencing (WGS), non-human resequencing (INVIEW Resequencing for plants, animals, yeast, and bacteria), Whole Exome Sequencing (INVIEW Human Exome), ChIP-seq, Whole Genome Bisulfite Sequencing (INVIEW Epigenome), Olink Explore and SOMAmer plasma proteomics, 16S/18S/ITS amplicon profiling (INVIEW Microbiome), and whole-genome shotgun metagenomics. Spatial transcriptomics, standalone ATAC-seq, and standalone metabolomics are not publicly specified as standard INVIEW catalog services. For dry-lab re-analysis projects, they accept pre-existing FASTQ, BAM, or VCF files.
Secondary pipelines process data using established open-source tools such as FastQC, MultiQC, Cutadapt, Trimmomatic, BWA, Bowtie2, STAR, HISAT2, featureCounts, HTSeq, DESeq2, edgeR, GATK, Samtools, FreeBayes, SPAdes, Velvet, QIIME2, Mothur, and MACS2. Software tool names and version numbers are documented in final project reports.
Deliverables include raw FASTQ files, aligned BAM/CRAM files, annotated VCF variant files, expression count matrices, BED peak files, and summary execution reports in HTML and PDF formats. Raw data and analysis files are hosted on the myEOL portal with a standard download retention window of 100 days (or 14 to 30 days depending on contract terms), after which files are archived or removed. Internal R/Python scripts, Nextflow workflows, and container definitions are retained internally and are not handed over to clients.
What Pepkio Does
Pepkio provides dry-lab bioinformatics analysis for research groups that already have raw data files, such as FASTQ reads, aligned BAM files, VCF variant calls, or count matrices. The service covers bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics (10x Visium/Visium HD), WGS/WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics across human, rodent, plant, agricultural, and microbial datasets.
Workflows use standard open-source software such as STAR, fastp, DESeq2, Seurat, MACS2, and GATK. Deliverables include executable R and Python scripts, parameter logs, normalized count matrices, editable publication-ready vector figures (PDF and SVG formats), optional Nextflow or Snakemake workflow manager scripts, optional Docker or Conda container specifications, and a drafted Methods section for manuscript submission.
Projects include 1-on-1 collaboration with the senior computational biologist handling the dataset. Researchers discuss experimental parameters during initial scoping, receive custom script adjustments during execution, and can get technical help when addressing peer-reviewer comments after manuscript submission.
Eurofins Genomics vs Pepkio: Head-to-Head Comparison
What analysis types and organisms do they support?
Eurofins Genomics provides end-to-end wet-lab sequencing combined with secondary bioinformatics across human, model animal, crop, livestock, microbial, and viral samples. Their wet-lab capabilities support specialized assays such as high-multiplex Olink Explore and SOMAmer protein profiling alongside short-read Illumina and long-read Oxford Nanopore sequencing.
Pepkio works on existing data files across bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics in human, agricultural, and model species.
How transparent are the bioinformatics pipelines?
Pepkio hands over the R and Python execution scripts, parameter logs, reference genome build details, and software tool versions. Researchers can inspect the code used in statistical testing and visualization.
Eurofins Genomics lists tool names (such as STAR, DESeq2, GATK, and QIIME2), parameter settings, and reference builds inside final HTML and PDF project reports. Software tool versions are documented in delivered project reports. Eurofins Genomics runs managed internal BioIT workflows and does not share raw execution scripts or underlying workflow source code.
How do they handle code delivery and reproducibility?
Pepkio supplies runnable source code and environment specifications so researchers can execute pipelines locally on their own computational infrastructure. Deliverables include raw R and Python scripts, version-pinned environment files, optional Nextflow or Snakemake scripts, and optional Docker or Conda containers.
Eurofins Genomics delivers raw FASTQ files, aligned BAM/CRAM files, variant VCF files, summary data tables, and execution reports via secure download links or myEOL. Executable scripts, workflow definition files, and container definitions are not distributed to clients.
What publication and reviewer support is included?
Pepkio supplies high-resolution editable vector graphics (PDF and SVG), a draft Methods section written for journal submission, and technical support from the lead computational biologist to address peer-reviewer questions or run requested re-analyses.
Eurofins Genomics provides static figures (heatmaps, volcano plots, PCA plots, coverage tracks) in PDF, SVG, and PNG formats inside project reports, along with structured methodology descriptions and tool citations suitable for adaptation into manuscript Methods sections. Eurofins Genomics technical support can clarify pipeline parameters if questioned by reviewers, though formal written responses or free re-analysis rounds are handled on a case-by-case basis via project quote updates. Academic co-authorship is not required by Eurofins Genomics.
How do turnaround times and deadlines compare?
Eurofins Genomics offers rapid turnaround for routine wet-lab services, such as 1 to 2 business days for Sanger sequencing and plasmid reads, 2 to 5 business days for bacterial WGS, and 10 to 14 business days for 16S microbiome profiling. Standard NGS runs (mRNA-seq, WGS/WES) and custom BioIT projects take 2 to 4 weeks (10 to 20 business days).
Pepkio completes standard dry-lab cohorts in 2 to 4 weeks and complex multi-contrast studies in 4 to 6 weeks, with time for custom script modifications, parameter optimization, and quality checks.
What is the communication model with analysts?
Pepkio connects researchers with the computational biologist executing their analysis via email, video calls, or direct messaging throughout project scoping, execution, and post-delivery review.
Eurofins Genomics routes project updates, order tracking, and technical inquiries through an assigned Project Manager or Customer Support Representative. Direct consultations with bioinformaticians can be scheduled for specialized custom scoping discussions.
How does pricing compare?
Both options use quote-based pricing for NGS and custom bioinformatics projects rather than fixed online price lists. Eurofins Genomics quotes cover sample preparation, sequencing, primary/secondary bioinformatics processing, summary HTML/PDF reports, and standard file delivery (FASTQ, BAM, VCF). Custom pipeline development, non-standard visualisations, expedited processing, and extended data retention beyond the standard window incur extra fees.
Pepkio provides fixed-price project quotes scoped upfront that include script handover, editable vector figures, draft Methods text, and post-delivery reviewer support without speed surcharges.
How is data security and file retention managed?
Eurofins Genomics hosts raw sequencing files and report outputs on the myEOL portal with a download window of 100 days (or 14 to 30 days depending on contract terms), requiring clients to download and store their data before links expire. Physical DNA and RNA samples are stored for 4 weeks (or 10 days for express runs) before disposal. Clients own raw data and derived analytical tables, while internal BioIT pipeline code remains Eurofins' property.
Pepkio transfers final output files, R/Python scripts, figures, and documentation upon project completion. Clients own the data, code, and intellectual property, and there is no portal download expiration window.
How are custom or non-standard analyses handled?
Pepkio modifies R and Python scripts during initial project scoping to accommodate unique experimental designs, custom reference genomes, or non-standard statistical models, handing over custom code upon completion.
Eurofins Genomics executes standardized automated pipelines for established reference builds; complex multi-factorial designs or bespoke algorithm development are scoped separately as advanced custom bioinformatics add-ons.
When Pepkio Is the Better Fit
- You already have raw FASTQ, BAM, VCF, or count files and need dry-lab bioinformatics analysis.
- Your project requires executable R and Python scripts, parameter logs, or optional container recipes to run pipelines locally on your institution's HPC.
- You want ongoing collaboration with the computational biologist executing your data analysis.
- You need editable vector figures (SVG/PDF) and a draft Methods section written for manuscript submission.
- You want post-delivery technical support from the lead analyst to address journal reviewer queries or run requested re-analyses.
When Eurofins Genomics Is the Better Fit
- You need an integrated provider to handle physical sample extraction, library preparation, high-throughput sequencing, and secondary bioinformatics reporting under one roof.
- Your study involves high-multiplex protein biomarker discovery using the Olink Explore or SOMAmer plasma proteomics platforms.
- You require certified global laboratory infrastructure with fast turnaround for routine plasmid or Sanger sequencing.
- You prefer standardized HTML/PDF execution reports and portal-based sample tracking without handling local code execution.
- Your lab is submitting large sample cohorts that benefit from volume-based per-sample sequencing pricing.
Trade-Offs at a Glance
| Consideration | Pepkio | Eurofins Genomics |
|---|---|---|
| Wet-lab sequencing | Requires pre-existing data files; no physical wet-lab sample processing | Full wet-lab sequencing infrastructure (Illumina, Nanopore, MGI) and sample preparation |
| Code delivery | Executable R/Python scripts, workflow files, and container recipes handed over | Proprietary internal BioIT pipelines; delivers reports and data tables without raw code |
| Analyst access | 1-on-1 access to the computational biologist handling your data | Primary communication managed through an assigned Project Manager |
| Data retention | Direct file handover with no portal download expiration | myEOL download portal retention window of 100 days (or 14–30 days depending on contract) |
| Specialized assays | Focuses on core NGS, spatial transcriptomics, and omics modalities | Offers Olink and SOMAmer proteomics alongside standard transcriptomic and genomic INVIEW packages |
Frequently Asked Questions
Do I get the raw R or Python scripts used for my analysis?
Pepkio delivers executable R and Python scripts, parameter logs, and optional container recipes alongside final data tables and figures. Eurofins Genomics operates managed internal BioIT infrastructure and delivers summary HTML/PDF reports, BAM/VCF files, and count matrices, but does not share underlying R/Python execution scripts or workflow code.
Can Eurofins Genomics handle physical sample extraction and sequencing alongside bioinformatics?
Yes. Eurofins Genomics is a global contract research organization with laboratory facilities that include Illumina NovaSeq X Plus, Oxford Nanopore, and MGI sequencers. They process physical samples, such as blood, tissue, FFPE sections, and microbial cultures, for library preparation, sequencing, and primary/secondary bioinformatics. Pepkio operates as a dry-lab computational service for pre-existing data files.
Will either service help me respond to Reviewer 2's comments?
Pepkio includes technical support from the lead computational biologist to answer peer-reviewer questions, clarify methodology details, or execute requested re-analyses post-submission. Eurofins Genomics technical representatives can clarify report metrics and parameter settings if questioned by reviewers, but formal written responses or free re-analysis rounds are handled case-by-case via quote updates.
How long do I have to download my data files after project completion?
Eurofins Genomics hosts raw sequencing data and analysis deliverables on their myEOL online portal for a standard retention window of 100 days (or 14 to 30 days depending on regional contract terms), after which files are removed unless extended storage is purchased. Pepkio transfers scripts, tables, figures, and documentation upon project completion without portal expiration limits.
Can I run the analysis pipeline locally on my own institution's HPC cluster?
With Pepkio, yes. Deliverables include executable R and Python scripts, version-pinned environment files, and optional Nextflow, Snakemake, Docker, or Conda configurations designed for local execution. Eurofins Genomics pipelines run on internal BioIT infrastructure and are not exported for local cluster execution.
What formats are delivered for publication figures?
Pepkio provides high-resolution editable vector graphics (PDF and SVG) alongside standard raster files (PNG and TIFF), so researchers can modify labels, font sizes, and color palettes. Eurofins Genomics delivers static visualizations (heatmaps, volcano plots, PCA plots) embedded in analysis reports, exportable in PNG, PDF, and SVG formats.
Do I need to include Eurofins Genomics or Pepkio bioinformaticians as co-authors on my paper?
No. Standard commercial CRO terms apply for both services; co-authorship is not required for routine contract bioinformatics or sequencing analyses. Acknowledging the provider in your manuscript's Acknowledgments section is standard academic practice.
What sequencing platforms does Eurofins Genomics use for wet-lab projects?
Eurofins Genomics operates high-throughput Illumina instruments (such as the NovaSeq X Plus and NovaSeq 6000), Oxford Nanopore Technologies platforms (GridION and PromethION for long-read sequencing), and MGI DNBSEQ-T7 sequencers.
What input files do I need to provide for Pepkio's dry-lab service?
Pepkio accepts raw FASTQ files from any sequencing platform, aligned BAM/CRAM files, VCF variant files, gene expression count matrices, or normalized proteomics data tables.
How does communication work during the project execution phase?
With Pepkio, you communicate with the senior computational biologist executing your analysis via email, video calls, or direct messaging. With Eurofins Genomics, routine updates and technical queries are routed through an assigned Project Manager or Support Representative, with technical consultation calls arranged during scoping for custom projects.
Are software tool names and versions documented in project reports?
Yes. Both services document tool names, parameter settings, and reference genome builds in project deliverables. Software tool versions are documented in delivered project reports by both Eurofins Genomics and Pepkio.
Bottom Line
Choose Eurofins Genomics when your laboratory needs a wet-lab partner to extract DNA/RNA, prepare libraries, sequence samples on Illumina or Nanopore platforms, and generate standardized HTML/PDF secondary bioinformatics reports. Choose Pepkio when you already have raw sequencing data and want a dry-lab computational partner that hands over executable R and Python scripts, provides publication-ready vector figures, offers 1-on-1 analyst collaboration, and provides post-submission reviewer support.
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