CD Genomics vs Pepkio: Bioinformatics Service Comparison

Quick Comparison Table

What CD Genomics Does

CD Genomics provides integrated wet-lab sequencing alongside standardized dry-lab bioinformatics analyses. Physical sample inputs, including fresh or frozen tissues, FFPE sections, cultured cell lines, blood, extracted DNA/RNA, and environmental samples, are processed using sequencing platforms such as Illumina NovaSeq, PacBio Revio, Oxford Nanopore PromethION, and 10x Genomics Chromium. For dry-lab requests on existing data, they accept raw FASTQ files, aligned BAM/CRAM files, VCF variant files, or count matrices.

Their dry-lab portfolio covers bulk RNA-seq (mRNA-seq, total RNA-seq, non-coding RNA, prokaryotic RNA-seq, metatranscriptomics, Ribo-seq), single-cell and spatial biology (scRNA-seq via 10x Genomics Chromium and PIP-seq, snRNA-seq, scATAC-seq, 10x Visium spatial transcriptomics), Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) with de novo assembly and variant calling, epigenomics (ChIP-seq, ATAC-seq, CUT&Tag, WGBS, RRBS, MeDIP-seq), quantitative proteomics (TMT, DIA, LC-MS/MS), untargeted and targeted metabolomics, microbiome profiling (16S/18S/ITS amplicon, shotgun metagenomics, AMR profiling), long-read omics (PacBio SMRT, Nanopore direct RNA/DNA), and multi-omics data integration.

Pipelines rely on open-source tools cited in project documentation, including FastQC, Trimmomatic, Cutadapt, STAR, HISAT2, Bowtie2, BWA, featureCounts, HTSeq, DESeq2, edgeR, limma-voom, CellRanger, Seurat, MACS2, GATK, FreeBayes, Samtools, SPAdes, Canu, QIIME2, Mothur, BLAST, Diamond, InterProScan, and Staramr. Software tool versions are documented in delivered project reports. Deliverables include raw FASTQ files, aligned BAM/CRAM files, annotated VCF files, normalized count tables, summary HTML and PDF reports, and login credentials for the CD Genomics Bioinformatics Cloud Platform. CD Genomics operates as a managed service and does not distribute raw execution scripts (R/Python), internal shell scripts, workflow manager files (Nextflow/Snakemake), or container recipes to clients.

What Pepkio Does

Pepkio provides dry-lab bioinformatics services for research groups that already have raw data files, such as FASTQ sequencing reads, BAM alignment files, or raw count matrices. Dry-lab 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, non-model crop, and microbial datasets.

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

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

CD Genomics vs Pepkio: Head-to-Head Comparison

How do analysis scope and organism support compare?

CD Genomics processes physical biological samples and executes wet-lab library preparation and high-throughput sequencing alongside dry-lab analysis across a wide range of experimental assays. Researchers can submit biological inputs, such as tissue, blood, or environmental samples, and receive sequencing coupled with primary bioinformatics. Their scope includes specialized wet-lab omics like WGBS/RRBS bisulfite sequencing, Ribo-seq, Nanopore direct RNA sequencing, and LC-MS/MS proteomics across human, model organisms, non-model agricultural crops, livestock, marine species, and microbes.

Pepkio accepts pre-existing digital data files (FASTQ, BAM, VCF, or count matrices) and performs dry-lab computation for bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, WGS/WES, ChIP-seq, ATAC-seq, metagenomics, and proteomics across human, model organisms, agricultural crops, and microbial genomes.

How transparent are pipeline tools and software specifications?

Pepkio delivers the underlying analysis scripts. When your analysis completes, you receive the R scripts, Python pipeline, command-line parameter log, and software version numbers used during execution.

CD Genomics outlines pipeline steps, reference genome builds, software tools (such as STAR, HISAT2, DESeq2, Seurat, or GATK), and quality control statistics inside HTML and PDF reports. Software tool versions are documented in delivered project reports. Because CD Genomics runs managed infrastructure pipelines, raw execution scripts and underlying workflow code are not shared.

How do the services handle code delivery and reproducibility?

Pepkio delivers runnable source code and environment definitions so you can execute the pipeline on your local cluster or workstation. Deliverables include executable R and Python scripts, parameter logs, version-pinned environment files, optional Nextflow or Snakemake workflow manager files, and optional Docker or Conda container specifications.

CD Genomics provides raw FASTQ reads, aligned BAM files, VCF files, count matrices, summary reports, and login credentials to the CD Genomics Bioinformatics Cloud Platform. They do not deliver raw execution scripts, shell files, workflow scripts, or container recipes for local execution.

What publication support is included for figures, Methods, and reviews?

Pepkio delivers high-resolution editable vector graphics (PDF, SVG), a drafted Methods section ready for manuscript submission, and post-delivery technical support from the lead computational biologist to handle reviewer comments or run requested re-analyses.

CD Genomics supplies static visualizations in final reports and allows you to adjust plot parameters, filter thresholds, and export figures (PDF, SVG, PNG) through the CD Genomics Bioinformatics Cloud Platform. Reports contain structured methodology text and parameter notes that you can adapt for publication. Technical specialists clarify report details if questioned by peer reviewers, while formal written responses or re-analyses are handled on a project-by-project basis.

What are the expected turnarounds and timeline constraints?

CD Genomics delivers standard NGS sequencing and bioinformatics results in 2 to 4 weeks (10 to 15 business days) after sample QC verification. Expedited processing can be requested during initial project scoping.

Pepkio completes standard dry-lab cohorts in 2 to 4 weeks, with complex multi-contrast studies taking 4 to 6 weeks. This timeline covers custom script refinement, parameter tuning, and quality verification.

How does client communication work during a project?

Pepkio pairs you with the lead computational biologist executing your data analysis. You communicate via email, video meetings, or messaging throughout scoping, execution, and post-delivery review.

CD Genomics routes project communication, sample tracking, and technical inquiries through an assigned Project Manager who coordinates with internal technical teams. Direct video calls with bioinformaticians can be arranged during custom project design.

How is pricing structured, and what is included?

Pepkio provides fixed-price upfront project quotes that cover data processing, full script delivery, editable vector figures, draft Methods text, and post-delivery reviewer support.

CD Genomics operates a quote-based pricing model per sample or per project scope, with volume discounts for large sample numbers. Prices are not listed publicly online. Base quotes include sample QC, sequencing, raw data delivery, standard pipeline execution, HTML summary reports, and cloud platform access. Custom bioinformatics, extended data storage beyond 3 months, and extra re-analysis rounds incur extra charges.

How are data ownership and file security managed?

CD Genomics hosts generated sequencing data and report files on cloud servers with 3 months of free storage following data generation. Physical sample retention timelines post-project are not publicly specified. Clients own raw sequencing files and final derived tables/reports, while internal pipeline scripts and cloud software remain proprietary.

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

How are custom or non-standard analyses handled?

Pepkio customizes R and Python scripts during initial scoping to accommodate non-standard experimental designs, custom reference genomes, or bespoke statistical models, delivering custom code upon completion.

CD Genomics processes standard reference assemblies using automated pipelines. Requests for custom exploratory plots, non-standard workflow modifications, or advanced multi-omics integrations are handled as custom bioinformatics add-ons or explored using the interactive cloud platform.

When Pepkio Is the Better Fit

• You already have FASTQ, BAM, VCF, or count files and only need dry-lab computational analysis.
• You require executable R and Python scripts, parameter logs, or optional container recipes for local rerun and code reproducibility.
• You want continuous contact with the computational biologist carrying out your analysis.
• You need editable vector graphics (PDF/SVG) and a fully drafted Methods section for manuscript submission.
• You want post-delivery support from the lead analyst to address journal reviewer comments or execute requested re-analyses.

When CD Genomics Is the Better Fit

• You need an integrated wet-lab and dry-lab provider to handle biological sample extraction, library preparation, multi-platform sequencing (Illumina, PacBio, Nanopore), and primary bioinformatics.
• Your project requires specialized wet-lab omics assays such as Ribo-seq, WGBS/RRBS bisulfite sequencing, Nanopore direct RNA sequencing, or LC-MS/MS proteomics.
• You prefer interactive web tools like the CD Genomics Bioinformatics Cloud Platform to explore differential expression tables and adjust plot styling without writing code.
• You need standard sequencing and bioinformatics turnaround within 10 to 15 business days post-QC.
• You are submitting large sample batches that benefit from volume-based per-sample quotes.

Frequently Asked Questions

Do I get the raw R or Python execution scripts for my analysis?

Pepkio delivers the underlying R and Python scripts, parameter logs, and optional workflow manager files (Nextflow/Snakemake) with every project. CD Genomics provides final reports, data tables, BAM/VCF files, and interactive cloud access, but does not share raw execution scripts or pipeline source code.

Will either team assist with Reviewer 2's methodological comments?

Pepkio includes technical support from the lead computational biologist who executed your analysis to help draft responses and perform requested re-analyses. CD Genomics provides technical project support to clarify pipeline details and parameter choices, with formal written responses or re-analyses handled on a project-by-project basis.

What data files do I need to supply if I already have sequencing data?

Both services accept standard digital formats including raw FASTQ files, aligned BAM/CRAM files, variant VCF files, or expression count matrices. Pepkio operates on existing data files, whereas CD Genomics can accept either raw biological samples for full wet-lab processing or pre-existing digital files for standalone bioinformatics.

How long will I wait to receive my finished bioinformatics analysis?

CD Genomics typically completes standard NGS sequencing and bioinformatics projects in 2 to 4 weeks (10 to 15 business days) post-QC verification, with expedited turnaround available upon request. Pepkio completes standard dry-lab cohorts in 2 to 4 weeks and complex multi-contrast studies in 4 to 6 weeks.

Can I edit the final figures to fit journal formatting guidelines?

Pepkio delivers high-resolution vector figures in PDF and SVG formats that can be opened and edited in vector graphics software. CD Genomics provides static plots in PDF/HTML reports alongside the interactive CD Genomics Bioinformatics Cloud Platform, where you can modify visual parameters and export PDF, PNG, or SVG figures.

Who will be my primary point of contact during the analysis?

With Pepkio, you communicate with the senior computational biologist executing your data analysis. With CD Genomics, primary communication is managed by an assigned Project Manager who coordinates with internal analysis teams, though video calls with bioinformaticians can be arranged during custom project scoping.

How long are data files and physical samples stored after delivery?

CD Genomics stores downloadable project data on cloud servers for 3 months post-generation at no extra cost. Physical sample retention timelines post-project are not publicly specified. Pepkio transfers final output files, scripts, and documentation upon completion for local archiving.

Is a drafted Methods section included for manuscript preparation?

Pepkio provides a drafted, manuscript-ready Methods section detailing tools, parameters, and reference genome builds. CD Genomics includes structured methodology descriptions, software tool citations, and parameter notes in final project reports that researchers can adapt into paper Methods sections.

How is pricing calculated, and are public price lists available?

Neither option publishes fixed price lists online. CD Genomics provides custom quotes based on sample count, sequencing depth, and analysis scope, offering volume discounts for large cohorts. Pepkio provides fixed upfront quotes for dry-lab project scopes without speed surcharges.

Can I obtain containerized environment files (Docker or Conda) to rerun the analysis locally?

Pepkio offers version-pinned environment files and optional Docker or Conda container specifications for local computational reproducibility. CD Genomics runs managed internal execution environments and does not distribute Docker, Singularity, or Conda recipes to clients.

Which option is better suited for non-model organisms or non-standard experimental designs?

Pepkio tailors R and Python scripts during project scoping to handle custom reference genomes, non-standard contrast matrices, or novel statistical models, delivering customized code upon completion. CD Genomics supports non-model crops, livestock, and marine species across their pipeline portfolio, with non-standard analytical requests handled as custom bioinformatics add-ons.

Can I analyze single-cell or spatial transcriptomics data with these options?

Yes, both options support single-cell and spatial omics. CD Genomics handles wet-lab library preparation (10x Genomics Chromium, PIP-seq) and spatial sequencing (10x Visium) alongside dry-lab cell clustering and marker identification. Pepkio performs dry-lab single-cell RNA-seq and spatial transcriptomics analysis (10x Visium/Visium HD) from existing sequencing files, delivering custom Seurat R code and vector plots.

Bottom Line

The choice between CD Genomics and Pepkio depends on whether your project needs wet-lab sample processing or custom dry-lab code delivery. If you need an end-to-end CRO to extract DNA/RNA, run sequencing across Illumina, PacBio, or Nanopore platforms, and explore figures in a cloud interface without writing code, CD Genomics may be the better fit. If you already have FASTQ, BAM, or count files and want dry-lab computation, R/Python script handover, computational biologist access, and manuscript support, Pepkio may be the better fit.