---
title: "BGI Genomics vs Pepkio: Bioinformatics Service Comparison"
contentType: "ARTICLE"
datePublished: "2026-08-06"
dateModified: "2026-08-06"
canonicalUrl: "/compare/pepkio-vs-bgi-genomics"
---

# BGI Genomics vs Pepkio: Bioinformatics Service Comparison

The choice between BGI Genomics and Pepkio depends on whether your study requires integrated wet-lab sequencing with web-based visualization or dedicated dry-lab analysis with complete executable source code. In this BGI Genomics vs Pepkio comparison, BGI Genomics provides physical sample extraction, library preparation, and high-throughput DNBSEQ sequencing alongside managed secondary analysis, delivering processed data tables and interactive web dashboards within 18 to 40 business days. Pepkio focuses exclusively on dry-lab bioinformatics for existing FASTQ, BAM, or count datasets, delivering executable R and Python scripts, version-pinned environment files, editable vector figures, and draft Methods sections within 2 to 4 weeks, with optional Nextflow or Snakemake workflows and Docker or Conda containers. Choose BGI Genomics when you require large-scale wet-lab sequencing, proprietary Stereo-seq spatial transcriptomics, or code-free cloud data exploration. Choose Pepkio when you already have sequencing data and need pipeline transparency, direct computational biologist access, and hands-on reviewer response support.

## Quick Comparison Table

| Aspect | Pepkio | BGI Genomics |
| --- | --- | --- |
| Primary service scope | Dedicated dry-lab computational analysis for existing sequencing data | Integrated wet-lab sample processing, DNBSEQ sequencing, and dry-lab secondary analysis |
| Supported analyses | Bulk [RNA-seq](/services/rna-seq), [single-cell RNA-seq](/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](/services/atac-seq), [metagenomics](/services/metagenomics), [proteomics](/services/proteomics) | Bulk RNA-seq (mRNA, miRNA, lncRNA, circRNA), single-cell & spatial (scRNA-seq, scDNA-seq, Stereo-seq), WGS/WES, epigenomics (ChIP-seq, ATAC-seq, WGBS, RRBS), proteomics/metabolomics, microbiome (16S, shotgun) |
| Pipeline tools & transparency | Standard open-source tools (STAR, DESeq2, Seurat, GATK) with exact tool versions documented in project deliverables | Standard open-source tools (STAR, HISAT2, BWA, GATK, DESeq2) and proprietary software (Dr. Tom, DNBelab) documented in project reports |
| Code & workflow deliverables | Executable R and Python scripts; optional Nextflow or Snakemake workflows and optional Docker or Conda containers | Summary reports (PDF/Excel), processed data tables, BAM/VCF files, and Dr. Tom portal credentials; raw execution scripts are not delivered |
| Reproducibility approach | Source code handover, parameter logging, version-pinned environments, optional container recipes | Managed cloud infrastructure, summary reports, and processed data tables; workflow scripts and containers are not distributed |
| Figure deliverables | High-resolution editable vector graphics (PDF, SVG) and raster formats (PNG, TIFF) | PDF report visualizations and interactive figure customization and export (PDF, SVG, PNG) via Dr. Tom |
| Methods-section support | Drafted, publication-ready Methods section detailing software, parameters, reference builds, and citations | Structured methodology summaries, software tool citations, and parameter notes included in project reports |
| Reviewer-response support | Direct technical support from the lead bioinformatician for reviewer queries and re-analyses | Ph.D. technical support to clarify reports and tables; written reviewer responses or major re-analyses handled via quote updates |
| Turnaround time | 2–4 weeks for standard cohorts; 4–6 weeks for complex multi-contrast studies | ~18 business days post-QC for WGS, ~30 business days for bulk RNA-seq, ~40 business days for scRNA-seq |
| Analyst interaction model | Direct contact with the lead computational biologist executing the analysis | Primary communication routed through an assigned Project Manager; technical specialists join scoping or data review calls |
| Pricing structure | Fixed-price project quotes scoped upfront | Quote-based pricing per sample or project; volume-based tiered discounts available |
| Data ownership & storage | 100% client-owned data, code, figures, and IP; no download expiration | Client-owned sample data, raw files, and reports; internal pipeline software and Dr. Tom platform remain proprietary |
| Best suited for | Labs with raw data needing dry-lab analysis, code delivery, direct analyst collaboration, and manuscript support | Labs needing combined wet-lab sequencing and dry-lab reporting, high-throughput capacity, Stereo-seq spatial biology, or code-free cloud data exploration |

## What BGI Genomics Does
BGI Genomics provides high-throughput wet-lab sequencing alongside managed secondary bioinformatics analyses. Their facilities process inputs including fresh or frozen tissues, cell lines, FFPE tissue sections, blood, biofluids, extracted DNA or RNA, and low-input samples using DNBSEQ sequencing platforms developed by MGI Tech alongside Illumina systems. Bioinformatics coverage includes bulk RNA-seq (mRNA, miRNA, lncRNA, circRNA, differential expression, alternative splicing, GO/KEGG enrichment), single-cell transcriptomics (scRNA-seq, scDNA-seq via DNBelab C-Series or 10x Genomics), spatial transcriptomics via their proprietary Stereo-seq platform, Whole Genome Sequencing ([WGS](/services/variant-calling)) and Exome Sequencing (WES), epigenomics ([ChIP-seq](/services/chip-seq), [ATAC-seq](/services/atac-seq), WGBS, RRBS), quantitative [proteomics](/services/proteomics) (DIA, TMT), metabolomics, 16S/shotgun [metagenomics](/services/metagenomics), and multi-omics integration via the Dr. Tom system.

Data processing uses standard open-source packages alongside proprietary software, including FastQC, STAR, HISAT2, Bowtie2, BWA, GATK, FreeBayes, Strelka, featureCounts, DESeq2, edgeR, CellRanger, and the Dr. Tom Multi-Omics Data Mining System. Software tool versions are documented in delivered project reports. Deliverables include raw FASTQ files, aligned BAM/CRAM files, annotated VCF files, gene expression count matrices, structured PDF/Excel summary reports, and login credentials for the web-based Dr. Tom platform.

Researchers select BGI Genomics primarily for large-scale projects where wet-lab sample extraction and high-throughput sequencing are bundled with secondary data processing. The service operates as a managed platform where users explore differential expression tables, filter pathways, and generate plots inside the Dr. Tom web dashboard. BGI Genomics does not distribute raw execution scripts (R or Python), command-line shell scripts, workflow manager files (Nextflow or Snakemake), or container recipes to clients.

## What Pepkio Does
Pepkio provides dedicated dry-lab [bioinformatics analysis](/services/rna-seq) for research groups that already have raw data files, such as FASTQ sequencing reads, BAM alignment files, or count matrices. Analysis capabilities cover [bulk RNA-seq](/services/rna-seq), [single-cell RNA-seq](/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](/services/atac-seq), [metagenomics](/services/metagenomics), and [proteomics](/services/proteomics) across human, model organism, agricultural crop, and microbial datasets.

Workflows rely on established open-source software such as STAR, fastp, DESeq2, Seurat, MACS2, and GATK. Pepkio hands over executable R and Python scripts, parameter logs, normalized expression tables, publication-ready vector figures (PDF/SVG), and a draft Methods section written for manuscript submission. Optional Nextflow or Snakemake workflow manager files and optional Docker or Conda container specifications can be included for automated pipeline execution.

Projects follow a direct collaboration structure. Researchers work directly with the senior computational biologist assigned to their project, enabling upfront parameter customization, iterative exploratory analyses, and direct technical assistance when responding to peer-reviewer questions post-submission.

## BGI Genomics vs Pepkio: Head-to-Head Comparison

### How Do Analysis Scope and Assays Compare?
BGI Genomics manages physical sample preparation and sequencing across a broad catalog of wet-lab assays. Their capabilities include specialized wet-lab multi-omics assays such as WGBS/RRBS bisulfite sequencing, DIA/TMT quantitative proteomics, untargeted metabolomics, and high-resolution spatial transcriptomics via their proprietary Stereo-seq platform. They process human, model animal, plant, livestock, and microbial samples across fresh/frozen tissue, FFPE, blood, biofluids, and low-input samples.

Pepkio focuses exclusively on dry-lab computational analysis for existing data files across bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics (10x Visium/Visium HD), WGS/WES, ChIP-seq, ATAC-seq, metagenomics, and proteomics. Pepkio supports human, standard model organisms, agricultural species, and microbial genomes.

### How Do Pipeline Transparency and Software Specifications Compare?
Pepkio delivers complete script-level transparency for every computational step. Project handovers include executable R and Python scripts, command-line parameter logs, reference assembly metadata, and exact software versions used during execution.

BGI Genomics documents software tools (such as STAR, HISAT2, BWA, GATK, and DESeq2), reference assemblies, and quality control metrics within delivered project reports and the Dr. Tom dashboard. Software tool versions are included in final project deliverables. Because BGI Genomics operates managed cloud workflows, raw execution scripts and underlying pipeline code are not distributed to clients.

### How Do Reproducibility and Deliverables Compare?
Pepkio delivers runnable source code and environment specifications to ensure local computational reproducibility. Clients receive raw R and Python scripts, version-pinned environment files, and optional Nextflow or Snakemake workflow scripts alongside optional Docker or Conda containers, allowing researchers to inspect, execute, or modify the analysis on local infrastructure.

BGI Genomics delivers raw FASTQ files, aligned BAM/CRAM files, variant VCF files, gene expression count matrices, and summary reports alongside Dr. Tom login credentials. BGI Genomics does not supply executable R or Python scripts, workflow manager code, or container recipes for local execution.

### What Publication Support Is Provided?
Pepkio provides manuscript-ready deliverables and direct technical support during peer review. Outputs include editable high-resolution vector graphics (PDF, SVG), a complete Methods section written for journal submission, and direct technical assistance from the lead bioinformatician to address reviewer comments or execute requested re-analyses.

BGI Genomics provides static summary plots in project reports and allows researchers to filter data, customize visual styles, and export high-resolution vector (PDF, SVG) or raster (PNG) files within Dr. Tom. Reports include structured methodology text, software tool citations, and parameter notes that authors can adapt for publication. Ph.D. technical specialists answer post-delivery questions regarding report data tables, while post-publication journal reviewer requests or extensive exploratory re-analyses are arranged via project scope updates.

### How Do Turnaround Times and Scheduling Compare?
BGI Genomics operates high-throughput workflows with turnaround times tied to wet-lab sequencing and pipeline processing. Standard turnaround post-QC acceptance is approximately 18 business days for Whole Genome Sequencing (with rapid options around 10 business days), 30 business days for bulk RNA-seq, 40 business days for single-cell RNA-seq, and 57 business days for single-cell DNA-seq.

Pepkio operates on fixed dry-lab project timelines, completing standard cohorts in 2 to 4 weeks and complex multi-contrast studies in 4 to 6 weeks. This timeline accommodates custom script adjustments, parameter optimization, and thorough quality checks.

### How Does Communication Work During a Project?
Pepkio connects researchers directly with the computational biologist executing their analysis. Communication occurs via email, video conference, or direct messaging throughout scoping, execution, and post-delivery review.

BGI Genomics routes project updates, sample tracking, and technical inquiries through an assigned Project Manager who coordinates with internal technical teams. Direct discussions with Ph.D. bioinformatics specialists occur primarily during initial scoping calls or scheduled post-delivery data interpretation sessions.

### How Do Pricing and Scope Inclusions Compare?
BGI Genomics uses a quote-based pricing model per sample or project, offering tiered volume discounts for large sequencing cohorts. Base quotes cover primary and secondary bioinformatics pipelines, Dr. Tom platform access, basic QC reports, standard differential expression or variant tables, secure data transfer, and post-delivery Ph.D. technical support. Expedited turnaround, custom non-standard pipelines, advanced multi-omics integration, extended cloud storage beyond the standard window, and additional re-analysis rounds incur extra fees.

Pepkio provides fixed-price project quotes scoped upfront before work begins. Quotes cover data processing, full script handover, editable vector figures, draft Methods text, and post-delivery reviewer support without speed surcharges or unexpected add-ons in a [bioinformatics CRO](/services/cro) model.

### How Is Data Ownership and Storage Handled?
BGI Genomics hosts raw data (FASTQ, BAM) and report outputs on cloud servers for a temporary retention window (typically 30 days to 6 months post-delivery depending on regional contract terms), after which clients must maintain their own long-term copies. Clients own their physical sample data, raw sequencing files, and output reports, while BGI Genomics retains ownership of internal pipeline software and Dr. Tom platform code. Institutional compliance policies or procurement regulations may affect data transfer for certain academic or corporate institutions.

Pepkio transfers all final output files, R/Python scripts, and documentation directly upon project completion. Clients retain 100% ownership over all data, code, figures, and intellectual property without server download expiration constraints.

### Can Custom or Non-Standard Analyses Be Handled?
Pepkio customizes R and Python scripts during initial project scoping to support non-standard experimental designs, custom reference genomes, or novel statistical models, delivering all modified code upon completion.

BGI Genomics executes standardized automated pipelines for established reference assemblies. Non-standard experimental designs, custom algorithm development, or advanced multi-omics integrations are scoped separately as advanced bioinformatics add-ons or explored by the researcher within the code-free Dr. Tom platform.

## When to Choose Pepkio
- You already have raw FASTQ, BAM, VCF, or count files and need dedicated dry-lab analysis.
- You require executable R and Python scripts, parameter logs, or optional container recipes to maintain local computational reproducibility.
- You want direct, ongoing collaboration with the computational biologist executing your data analysis.
- You need publication-ready editable vector figures (SVG/PDF) and a fully drafted Methods section for manuscript submission.
- You want direct technical support from the lead analyst to address journal reviewer queries or run requested re-analyses.

## When to Choose BGI Genomics
- You need an all-in-one provider to handle physical sample extraction, library preparation, high-throughput DNBSEQ sequencing, and secondary bioinformatics reporting.
- Your project requires proprietary high-resolution spatial transcriptomics via Stereo-seq (STOmics) or specialized wet-lab assays like WGBS/RRBS bisulfite sequencing or DIA/TMT proteomics.
- You prefer a code-free interactive interface like Dr. Tom to explore differential expression tables, filter pathways, and export plots without writing code.
- You are submitting large sample batches that benefit from volume-based per-sample sequencing discounts.
- You require high-throughput sequencing capacity with integrated primary and secondary data processing under a single contract.

## Summary of Trade-Offs
- **Choosing Pepkio means**: You gain full R and Python script delivery, version-pinned environment files, editable vector figures, draft Methods text, and direct communication with your lead bioinformatician—but you must supply pre-existing FASTQ, BAM, or count data, as Pepkio does not provide wet-lab sample extraction, library preparation, or sequencing.
- **Choosing BGI Genomics means**: You gain complete wet-lab sample processing, low per-gigabase sequencing costs on DNBSEQ platforms, proprietary Stereo-seq spatial transcriptomics, and interactive web visualization via Dr. Tom—but your project communication passes through project managers, you do not receive raw executable R/Python scripts or container recipes, and cloud data retention is limited to a temporary storage window.

## 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 specs so your lab can inspect or rerun the workflow locally. BGI Genomics operates a managed service model that delivers processed data tables, alignment files, summary reports, and Dr. Tom credentials, but does not distribute internal pipeline scripts or source code.

### Will BGI Genomics or Pepkio write the Methods section for my manuscript?
Pepkio includes a drafted, publication-ready Methods section detailing reference assemblies, alignment tools, statistical cutoffs, and software packages used. BGI Genomics provides structured methodology summaries, software tool citations, and parameter notes within final analysis reports and the Dr. Tom platform, which researchers can adapt into their manuscript.

### How do both options handle journal Reviewer 2 comments during peer review?
Pepkio provides direct post-delivery technical support from the lead bioinformatician to help address reviewer queries or execute requested re-analyses. BGI Genomics Ph.D. technical support specialists answer questions regarding report metrics and data tables, while formal written responses or re-analysis rounds outside the initial project proposal are handled via quote updates.

### Can I rerun the analysis on my own local HPC or server later?
With Pepkio, you can rerun the analysis locally using the delivered R and Python scripts alongside version-pinned environment files or optional containers. With BGI Genomics, you cannot rerun internal pipeline code locally, but you can filter differential expression results and adjust visualizations through the Dr. Tom platform.

### How long do I have to download my raw sequencing data and analysis files?
BGI Genomics hosts sequencing data (FASTQ, BAM) and report outputs on cloud servers for a temporary retention window (typically 30 days to 6 months post-delivery depending on regional contract terms), requiring clients to download and archive their files before the window expires. Pepkio transfers all final deliverables, scripts, and processed data directly upon project completion for permanent local archiving.

### Who will I speak with if I need help interpreting differential expression results?
With Pepkio, you communicate directly with the senior computational biologist who analyzed your dataset. With BGI Genomics, primary communication is routed through an assigned Project Manager who coordinates with internal technical teams, with Ph.D. technical specialists joining scheduled scoping or post-delivery consultation calls.

### What happens if my research involves a non-model organism or custom reference genome?
Pepkio customizes R and Python workflows during initial scoping to accommodate *de novo* transcriptome assemblies or custom reference genomes, delivering all modified scripts. BGI Genomics supports non-model organisms and custom references when assemblies are available, while non-standard pipeline development is scoped separately as an advanced bioinformatics add-on.

### Do I need to send physical biological samples, or can I submit raw FASTQ files?
BGI Genomics is a full-service wet-lab and dry-lab provider accepting biological samples (tissues, cell lines, FFPE, blood, extracted DNA/RNA), but also accepts raw FASTQ, BAM, or VCF files for standalone bioinformatics projects. Pepkio is strictly a dry-lab analysis service and accepts raw FASTQ, BAM, or count matrix files directly for computational processing.

### Can I customize figure colors, layout, and plot formatting for publication?
Pepkio provides high-resolution, editable vector files (PDF, SVG) alongside R/Python plotting scripts, giving you full freedom to modify layout, fonts, and aesthetics. BGI Genomics provides an interactive code-free interface inside Dr. Tom where users can filter gene lists, adjust visual parameters, and export high-resolution vector (PDF, SVG) or raster (PNG) figures.

### What is the typical turnaround time from data submission to receiving final results?
Pepkio completes dry-lab analyses in 2 to 4 weeks for standard cohorts and 4 to 6 weeks for complex multi-contrast designs. BGI Genomics standard turnaround post-QC is approximately 18 business days for Whole Genome Sequencing, 30 business days for bulk RNA-seq, 40 business days for scRNA-seq, and 57 business days for scDNA-seq.

### Are there extra charges if I need to re-cluster my single-cell dataset or change filter cutoffs?
BGI Genomics covers basic filtering and visualization adjustments within the interactive Dr. Tom platform, while major re-analysis rounds or custom parameter sweeps outside the initial proposal require separate quote updates. Pepkio includes parameter adjustments and iterative refinements within the initial fixed project scope.

### Do either BGI Genomics or Pepkio require co-authorship on publications?
Neither BGI Genomics nor Pepkio requires academic co-authorship for routine contract analysis. Standard academic practice is to acknowledge BGI Genomics ("BGI Genomics Co., Ltd.") or Pepkio in your manuscript's Acknowledgments section.

## Bottom Line
If your lab requires physical sample extraction, high-throughput DNBSEQ sequencing, proprietary Stereo-seq spatial biology, and an all-in-one wet-lab to dry-lab workflow with code-free cloud plotting via Dr. Tom, BGI Genomics is tailored for your study. If you already have raw sequencing data and require full R and Python script delivery, direct collaboration with lead bioinformaticians, and manuscript-ready Methods text, Pepkio provides the transparency and reproducibility needed for publication-focused research in this BGI Genomics vs Pepkio evaluation.


:::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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