Novogene vs Pepkio: Bioinformatics Service Comparison

Quick Comparison Table

What Novogene Does

Novogene provides high-throughput wet-lab sequencing alongside standardized dry-lab bioinformatics analyses. Their wet-lab facilities handle biological inputs including fresh or frozen tissues, FFPE sections, blood, cell lines, and extracted DNA or RNA using platforms such as Illumina NovaSeq X Plus, PacBio Revio, Oxford Nanopore PromethION, and 10x Genomics Chromium. For dry-lab pipelines, Novogene supports bulk RNA-seq (mRNA express, total RNA, non-coding RNA, prokaryotic), single-cell transcriptomics (10x Genomics Chromium, PIP-seq 3'), single-cell ATAC-seq, spatial transcriptomics (10x Visium), Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), epigenomics (ChIP-seq, ATAC-seq, CUT&Tag, WGBS, RRBS), quantitative proteomics (TMT, DIA, Olink), metabolomics, and 16S/shotgun metagenomics.

Pipeline processing relies on standard open-source tools detailed in project documentation, such as FastQC, Trimmomatic, STAR, HISAT2, Bowtie2, BWA, featureCounts, DESeq2, edgeR, CellRanger, Seurat, MACS2, and GATK. 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 HTML/PDF execution reports, and credentials for the web-based NovoMagic platform.

Novogene is typically selected by academic, clinical, and biotechnology researchers who require large-scale sequencing coupled with automated secondary data processing. The service operates under a managed model where clients can explore differential gene expression tables, filter threshold values, and export customized plots inside the NovoMagic portal. Novogene does not distribute raw execution scripts (R or Python), shell scripts, container recipes, or workflow source code to clients.

What Pepkio Does

Pepkio provides dedicated dry-lab bioinformatics analysis for research groups that already have raw data files, such as FASTQ sequencing reads, BAM alignment files, or raw count matrices. Analysis capabilities cover bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics (10x Visium/Visium HD), WGS and WES variant calling, ChIP-seq, ATAC-seq, metagenomics, and proteomics across human, model organism, agricultural crop, and microbial datasets.

Workflows build on open-source packages such as STAR, fastp, DESeq2, Seurat, MACS2, and GATK. Pepkio hands over full executable R and Python scripts, parameter logs, normalized expression tables, publication-ready vector figures (PDF/SVG), optional Nextflow or Snakemake workflow manager files, optional Docker or Conda container specs, and a draft Methods section written for manuscript submission.

Projects follow a direct collaboration structure. Researchers communicate directly with the senior computational biologist assigned to their project, allowing for upfront parameter adjustments, iterative custom analyses, and direct technical support when responding to peer-reviewer questions post-submission.

Novogene vs Pepkio: Head-to-Head Comparison

Analysis scope & organism support

Novogene handles physical sample processing and dry-lab analysis across a broader range of experimental assays than Pepkio. Their services combine sample extraction, library preparation, and high-throughput sequencing with secondary bioinformatics. Their catalog includes specialized wet-lab multi-omics assays such as WGBS/RRBS bisulfite sequencing, Olink proteomics, and untargeted metabolomics, supporting human, model animal, crop, marine, fungal, and microbial samples.

Pepkio focuses exclusively on dry-lab computation for existing data files across bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, WGS/WES, ChIP-seq, ATAC-seq, metagenomics, and proteomics. Analysis supports human, standard model organisms, non-model plants, and microbial genomes.

Pipeline transparency and software specifications

Pepkio provides complete code-level transparency for every analytical step. Deliverables include all raw R and Python scripts, command-line parameter logs, reference genome build notes, and exact software versions used during execution.

Novogene documents software tools (such as STAR, HISAT2, DESeq2, Seurat, and GATK), reference assemblies, and QC metrics within delivered PDF/HTML reports and the NovoMagic platform. Software tool versions are included in final project deliverables. Because Novogene runs managed infrastructure pipelines, raw execution scripts and underlying workflow code are not distributed.

Reproducibility & code delivery

Pepkio delivers runnable source code and environment specifications to ensure local reproducibility. Clients receive raw R and Python scripts, version-pinned environment files, optional Nextflow or Snakemake workflow scripts, and optional Docker or Conda containers. Researchers can execute, inspect, or modify the code directly on their own computational infrastructure.

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

Publication support: figures, Methods text, and reviewer responses

Pepkio provides manuscript-ready deliverables and direct support during peer review. Final outputs include editable high-resolution vector graphics (PDF, SVG), a complete Methods section written for journal submission, and direct technical support from the lead bioinformatician to address reviewer comments or perform requested re-analyses.

Novogene supplies static summary plots in project reports and allows researchers to adjust visual styles, filter thresholds, and export vector (PDF, SVG) or raster (PNG) files within NovoMagic. Reports include structured methodology text and parameter notes that authors can adapt for publication. While technical representatives can clarify report metrics, written reviewer responses and re-analyses are handled on a case-by-case basis.

Turnaround time & scheduling

Novogene offers faster turnaround for standard sequencing-coupled runs due to automated high-throughput operations. Pre-made library express sequencing is completed in 4 to 7 working days, while standard mRNA-seq, WGS, or scRNA-seq projects require 9 to 15 working days post-QC.

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 customization, parameter optimization, and thorough quality checks.

Communication model: analyst direct vs. project manager relay

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.

Novogene routes project updates, sample tracking, and technical inquiries through an assigned Project Manager who coordinates with internal technical teams. Direct discussions with bioinformaticians occur primarily during specialized scoping calls for custom projects.

Pricing structure & scope inclusions

Novogene uses a quote-based pricing model per sample or project, offering tiered volume discounts for large sample numbers. Base quotes cover sample processing, sequencing, raw data delivery, secondary pipelines, summary reports, and NovoMagic portal access. Advanced custom bioinformatics, expedited turnaround, and extended storage beyond 14–30 days incur additional 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.

Data retention & security

Novogene hosts raw data and report outputs on cloud servers with a download window of 14 to 30 days after project delivery. Clients must retrieve and archive their files within this window before links expire. Clients own their physical sample data, raw files, and report outputs, while Novogene retains ownership of internal pipeline software and NovoMagic platform code.

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.

Custom analysis & non-standard workflows

Pepkio customizes R and Python scripts during initial project scoping to support non-standard experimental designs, custom reference genomes, or novel statistical models. All customized code is handed over upon completion.

Novogene executes standardized automated pipelines for established reference assemblies. Non-standard experimental designs, custom algorithm development, or complex multi-omics integrations are scoped separately as advanced bioinformatics add-ons or explored by the client within the NovoMagic portal.

When Pepkio Is the Better Fit

• 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 post-delivery technical support from the lead analyst to address journal reviewer queries or run requested re-analyses.

When Novogene Is the Better Fit

• You need an all-in-one provider to handle physical sample extraction, library preparation, high-throughput NGS sequencing, and secondary bioinformatics reporting.
• Your study requires specialized wet-lab assays such as WGBS/RRBS bisulfite sequencing, Olink proteomics, or untargeted metabolomics.
• You prefer a code-free interactive interface like NovoMagic to explore differential expression tables and adjust plot styling without writing code.
• You require rapid turnaround times for pre-made library sequencing (4 to 7 working days) or standard sequencing runs (9 to 15 working days).
• You are submitting large sample batches that benefit from volume-based per-sample sequencing discounts.

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. Novogene operates a managed service model that delivers processed data tables, alignment files, summary reports, and NovoMagic credentials, but does not distribute internal pipeline scripts or source code.

Will Novogene 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. Novogene provides structured methodology text, software tool citations, and parameter notes within the final analysis report, which researchers can adapt into their manuscript.

How do both providers 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. Novogene technical support teams can clarify pipeline details and parameter settings if questioned by reviewers, while formal written responses or re-analysis rounds are handled on a case-by-case basis.

Can I rerun the analysis on my own 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 Novogene, you cannot rerun internal pipeline code locally, but you can re-filter differential expression results and adjust visualizations through the NovoMagic platform.

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

Novogene hosts sequencing data and report outputs on cloud servers for a download window of 14 to 30 days after project delivery, requiring clients to retrieve all files before links expire. Pepkio transfers all final deliverables, scripts, and processed data directly upon project completion for permanent local archiving.

Who will I talk to if I have questions about my data or differential expression results?

With Pepkio, you communicate directly with the senior computational biologist who analyzed your dataset. With Novogene, your primary point of contact is an assigned Project Manager who coordinates with internal technical teams, with technical specialists joining specific scoping calls when needed.

What happens if my study includes a non-model organism without a standard 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. Novogene supports non-model organisms provided a reference genome assembly is available, while non-standard workflow development is scoped separately as an advanced bioinformatics add-on.

Do I need to send physical samples, or can I send raw FASTQ files?

Novogene is primarily an end-to-end wet-lab provider accepting biological samples (tissues, cell lines, FFPE, blood, extracted DNA/RNA), but also accepts raw FASTQ, BAM, or VCF files for standalone dry-lab 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 thresholds 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. Novogene provides an interactive code-free interface inside NovoMagic where users can filter gene lists, adjust color palettes, and export vector or raster figures.

What is the typical turnaround time from raw 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. Novogene delivers pre-made library express sequencing results in 4 to 7 working days, and standard mRNA-seq, WGS, or scRNA-seq runs in 9 to 15 working days post-QC.

Are there extra fees if I need to re-cluster my single-cell dataset or change filter cutoffs?

Novogene covers basic threshold adjustments inside the self-service NovoMagic 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 Novogene or Pepkio require co-authorship on publications?

Neither Novogene nor Pepkio requires academic co-authorship for routine fee-for-service analysis. Standard academic practice is to acknowledge Novogene ("Novogene Co., Ltd.") or Pepkio in your manuscript's Acknowledgments section.

Bottom Line

If your lab needs physical sample extraction, high-throughput NGS sequencing, and an all-in-one wet-lab to dry-lab workflow with code-free cloud plotting via NovoMagic, Novogene is built for your pipeline. 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 control and transparency needed for publication-focused research in this Novogene vs Pepkio evaluation.