Macrogen vs Pepkio: Bioinformatics Service Comparison

Quick Comparison Table

What Services Does Macrogen Provide?

Macrogen operates global laboratory facilities that combine wet-lab processing with bioinformatics analysis. Researchers can submit physical specimens, including tissue, FFPE slides, cell lines, blood, or extracted nucleic acids, and can also submit external FASTQ, BAM, or VCF files for standalone dry-lab projects.

Its hardware includes Illumina (NovaSeq X, NovaSeq 6000, MiSeq), PacBio (Revio, Sequel IIe), Oxford Nanopore (PromethION, GridION), 10x Genomics Chromium, and MGI DNBSEQ platforms. Bioinformatics coverage includes bulk RNA-seq, single-cell transcriptomics (10x Visium, STOmics), WGS/WES variant calling, epigenomics (WGBS, RRBS, ChIP-seq, ATAC-seq), metagenomics, Olink proteomics, and metabolomics.

Workflows use standard open-source tools such as FastQC, STAR, BWA, DESeq2, GATK, CellRanger, Seurat, and MACS2. Deliverables include raw FASTQ files, aligned BAM files, VCFs, expression count tables, and structured PDF or HTML reports. Macrogen runs analyses on internal infrastructure and does not distribute internal R or Python execution scripts.

What Services Does Pepkio Provide?

Pepkio provides dry-lab bioinformatics analysis for teams that already have raw omics datasets. Inputs can include FASTQ files, BAM files, VCF datasets, or count matrices from external sequencing providers.

Supported analytical workflows include bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics (10x Visium and Visium HD), WGS and WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics. Pipelines incorporate standard open-source software such as STAR, fastp, DESeq2, Seurat, and GATK.

Deliverables include executable R and Python scripts, parameter logs, normalized data tables, editable vector figures (PDF and SVG), optional Nextflow or Snakemake workflows, optional Docker or Conda environment files, and a drafted Methods section. Teams communicate directly with the senior computational biologist running the analysis.

Pepkio vs Macrogen: Head-to-Head Comparison

Supported analysis types and organisms

Both providers work with standard model organisms, agricultural species, microbes, and non-model genomes using custom references. Macrogen runs physical sequencing instruments and supports wet-lab assays such as WGBS methylation, Olink proteomics, mass spectrometry metabolomics, and STOmics spatial transcriptomics. Pepkio focuses on dry-lab computation for external datasets across bulk RNA-seq, single-cell and spatial transcriptomics, WGS/WES, ChIP-seq, ATAC-seq, metagenomics, and proteomics.

Pipeline transparency and software execution

Pepkio hands over scripts, parameter logs, and environment configuration files that show filtering cutoffs, normalization choices, and statistical models. Macrogen lists software tools and major processing steps in final PDF/HTML reports, while internal pipeline code remains part of its managed infrastructure.

Reproducibility and code deliverables

Pepkio delivers executable R and Python scripts, parameter logs, version-pinned environments, and optional Nextflow, Snakemake, Docker, or Conda configs. This lets researchers inspect, edit, or rerun analyses locally. Macrogen provides processed tables (CSV/Excel), BAM/CRAM alignments, VCFs, and report visualizations, but not internal R/Python scripts or workflow source files.

Publication support and manuscript deliverables

Pepkio provides editable vector graphics (PDF, SVG), drafts a Methods section with software citations and parameters, and supports reviewer-response re-analyses. Macrogen includes figures in PDF/HTML reports, can provide plot tables or vector files on request, includes methodology summaries for manuscript preparation, and offers Ph.D. technical consultations.

Turnaround time and scheduling

Pepkio completes dry-lab analyses in 2 to 4 weeks for standard study cohorts and 4 to 6 weeks for complex multi-contrast projects. Macrogen's turnaround for combined sequencing and bioinformatics projects is 4 to 6 weeks following sample quality control approval, with 24 to 48 hours for Sanger sequencing, and 6+ weeks for complex multi-omics studies.

Analyst communication model

Pepkio gives direct access to the senior computational biologist running the analysis by email, video calls, or messaging. Macrogen routes most logistics through sales representatives and project managers, with Ph.D. technical specialists joining scoping and report-review calls.

Pricing structure

Neither provider publishes fixed price lists online; both issue project quotes following scoping. Macrogen quotes pricing per sample or project scope, with volume discounts available for large sample runs. Pepkio provides fixed upfront project quotes that cover data processing, script delivery, vector figure generation, Methods text drafting, and reviewer response support.

Data retention and ownership

Macrogen retains project data and reports for 90 days after release, keeps physical sequencing samples for 90 days, and keeps download links active for 2 weeks, with paid options for extended hosting. Pepkio transfers final deliverables, code, figures, and processed tables at completion and states client ownership of code, data, and related IP.

Custom analysis capabilities

Pepkio adapts R and Python code during scoping to support non-standard references, custom contrasts, or non-default statistical logic, and delivers the modified scripts. Macrogen handles non-standard analysis requests or custom reference assemblies through scope addenda and custom quotes.

When to Choose Pepkio

• You already have raw FASTQ, BAM, or count datasets and require dry-lab analysis without re-sequencing.
• Your project requires executable R or Python scripts to inspect parameters, modify plots, or integrate with internal pipelines.
• You want direct, ongoing communication with the computational biologist executing your data analysis.
• You need manuscript-ready vector figures (SVG/PDF) and a drafted Methods section for journal submission.
• You prefer fixed upfront project pricing that includes script handover and reviewer response support.

When to Choose Macrogen

• You need a single provider to manage physical sample extraction, library preparation, sequencing, and primary bioinformatics under one contract.
• Your study requires specific sequencing hardware such as PacBio HiFi, Oxford Nanopore PromethION, MGI DNBSEQ, or specialized assays like Olink proteomics.
• You require volume per-sample pricing discounts across large clinical or population cohorts.
• You prefer a managed reporting format (PDF/HTML reports and summary tables) without running or maintaining computational code locally.
• Your institution utilizes Macrogen's global network of laboratories and regional sample submission points.

Trade-Offs at a Glance

Frequently Asked Questions

Do I get the actual R or Python scripts used to process my data?

Pepkio delivers complete executable R and Python scripts, parameter logs, and optional Docker or Conda environment files so your team can rerun the analysis locally. Macrogen operates a managed service model that delivers processed data tables, alignment files, and PDF/HTML summary reports, but does not distribute internal execution code or pipeline scripts.

Will either service draft the Methods section for my manuscript?

Pepkio includes a draft publication-ready Methods section detailing reference assemblies, alignment software, filtering thresholds, and statistical packages used. Macrogen provides technical methodology summaries, tool lists, and key parameters within its project reports, which researchers can adapt into their manuscript Methods section.

How do both options handle journal reviewer comments or re-analysis requests?

Pepkio includes post-delivery technical support to assist with reviewer inquiries, run requested parameter modifications, and re-generate manuscript figures. Macrogen provides post-delivery consultations with Ph.D. technical specialists to address report questions; additional exploratory re-analyses or scope modifications are handled via project scope updates.

What happens if I already have raw FASTQ files from another sequencing facility?

Pepkio accepts external FASTQ files, BAM alignments, VCF files, or count matrices for standalone dry-lab analysis. Macrogen also accepts external FASTQ, BAM, VCF, or count files for standalone dry-lab projects alongside its core integrated sequencing services.

How long do I have to download my data after project completion?

Macrogen retains project data and analysis reports on its servers for 90 calendar days post-release, with download links active for 2 weeks; extended storage requires an additional fee. Pepkio transfers all final deliverables, code, and processed files upon project completion for immediate local archiving.

Can Macrogen handle wet-lab sample preparation and sequencing alongside bioinformatics?

Yes, Macrogen is an integrated genomics provider that handles physical sample extraction, library preparation, and sequencing across Illumina, PacBio, Oxford Nanopore, and 10x Genomics platforms alongside bioinformatic processing. Pepkio operates strictly as a dry-lab provider for datasets generated by external sequencing facilities.

How do I communicate with the person executing my analysis?

With Pepkio, you communicate directly with the senior computational biologist handling your dataset via email, video conference, or direct communication channels. Macrogen routes routine project updates through sales representatives and project managers, with Ph.D. technical specialists joining scoping and report review meetings.

Do I receive publication-ready vector figures for my manuscript?

Pepkio provides high-resolution, editable vector graphics (PDF and SVG) along with raster formats (PNG and TIFF). Macrogen includes data visualizations inside PDF/HTML project reports, and researchers can request raw plot data tables or vector files (SVG/PDF/EPS) for manuscript preparation.

What is the typical turnaround time for a bulk RNA-seq or variant calling project?

Pepkio delivers standard dry-lab analyses within 2 to 4 weeks from project kickoff. Macrogen's typical turnaround for integrated sequencing and bioinformatics projects is 4 to 6 weeks following sample quality control approval.

Are there restrictions on custom pipeline modifications or non-standard reference genomes?

Pepkio customizes R and Python execution scripts to accommodate non-standard reference genomes, custom statistical contrasts, or non-default filtering logic, delivering all custom code. Macrogen processes custom analysis requests or non-standard reference assemblies through project scope addenda and custom quotations.

How is project pricing structured for both options?

Neither provider publishes static pricing for custom bioinformatics work on public web pages. Both provide custom quotations based on project scope; Macrogen offers volume discounts per sample for large sequencing cohorts, while Pepkio provides fixed upfront project quotes covering processing, code delivery, Methods drafting, and reviewer support.

Do I retain full ownership of my analytical data and intellectual property?

Yes, both options grant research groups 100% ownership of physical sample data, raw sequencing files, and analytical results. Pepkio also transfers complete ownership of all custom executable scripts delivered with the project, whereas Macrogen retains proprietary ownership of its internal computational software and pipeline infrastructure.

Bottom Line

Choosing between Pepkio and Macrogen depends on whether you need integrated wet-lab sequencing services or dry-lab analysis with code-level handover. Macrogen is structured for physical sample processing plus managed reporting across sequencing platforms. Pepkio is structured for teams with existing raw data that want executable R/Python code, direct analyst communication, drafted Methods text, and editable vector figures.