LC Sciences vs Pepkio: Bioinformatics Service Comparison

Quick Comparison Table

What LC Sciences Does

LC Sciences runs an integrated wet-lab and dry-lab setup with over 300 computing nodes and 50 petabytes of storage. On the wet-lab side, they process physical samples, including fresh frozen tissue, cultured 2D/3D cells, FFPE sections, biofluids, and extracted nucleic acids, on instruments such as Illumina NovaSeq 6000, NovaSeq X Plus, 10x Genomics Chromium X, and automated UnityFX workstations. Their assays cover bulk RNA-seq (mRNA, total RNA, circRNA-seq, m6A-seq, degradome), specialized microRNA sequencing (miRNA-seq), single-cell RNA-seq, single-cell ATAC-seq, spatial transcriptomics (MERFISH, Stereo-seq, STARmap), WGS/WES variant calling, epigenomics (WGBS, RRBS, ChIP-seq, ATAC-seq), Olink proteomics, LC-MS/MS mass spectrometry quantitative proteomics, untargeted metabolomics, and 16S/18S/ITS or shotgun metagenomics.

For small RNA and microRNA profiling, LC Sciences uses its proprietary ACGT101 software suite (specifically ACGT101-miR). That pipeline handles adapter trimming, junk and low-complexity read filtering, non-coding RNA removal (rRNA, tRNA, snRNA, snoRNA), miRBase alignment, novel miRNA prediction, target gene prediction (TargetScan and MiRanda), and GO/KEGG functional enrichment. For general NGS assays, workflows use open-source tools such as FastQC, Cutadapt, STAR, Bowtie, DESeq2, edgeR, MACS2, Cell Ranger, and Seurat, with software versions documented in project reports.

Deliverables include raw FASTQ files via secure cloud download links, aligned BAM files, variant VCF files, gene and miRNA expression matrices (raw and normalized counts), peak-calling BED files, pathway tables, and HTML/PDF summary reports with publication-ready figures (heatmaps, volcano plots, PCA, and GO/KEGG plots in PDF, PNG, and SVG). LC Sciences is a managed CRO: they deliver processed data tables and reports, but do not share raw executable R/Python scripts, internal shell code, or container environments with clients.

What Pepkio Does

Pepkio provides dry-lab bioinformatics consulting for groups that already have raw sequencing files, such as FASTQ reads, aligned BAM files, or count matrices. Coverage includes 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, standard model organism, agricultural crop, and microbial datasets.

Workflows use peer-reviewed open-source tools including STAR, fastp, DESeq2, Seurat, MACS2, and GATK. Alongside processed outputs, Pepkio hands over runnable R and Python code, command-line parameter logs, version-pinned environment files, publication-ready vector figures (PDF/SVG), optional Nextflow or Snakemake workflow files, optional Docker or Conda container specifications, and a manuscript-ready Methods section written for journal submission.

Researchers communicate with the senior computational biologist assigned to the study through scoping, execution, and post-delivery review, including support for custom experimental designs and peer-reviewer queries.

Head-to-Head LC Sciences vs Pepkio Comparison

Which analyses, assays, and organisms are supported?

LC Sciences provides physical sample processing and dry-lab analysis across a wider range of specialized wet-lab assays than Pepkio. Their catalog includes degradome sequencing, m6A RNA-seq, circRNA-seq, WGBS/RRBS bisulfite sequencing, Olink proteomics, mass spectrometry metabolomics, and spatial imaging (MERFISH, Stereo-seq, STARmap). They process samples from human, mouse, rat, zebrafish, fruit fly, agricultural crops, livestock, marine species, fungi, and microbes.

Pepkio focuses on dry-lab computational workflows for existing data across bulk RNA-seq, single-cell RNA-seq, spatial transcriptomics, WGS/WES, ChIP-seq, ATAC-seq, metagenomics, and proteomics. Pepkio handles data from human, standard laboratory models, agricultural species, and non-model organisms when a reference assembly or transcript dataset is available.

How transparent are the bioinformatics pipelines?

Pepkio delivers the R and Python scripts, command-line parameters, reference genome build annotations, and software versions used during analysis.

LC Sciences lists software names (such as STAR, Bowtie, DESeq2, edgeR, MACS2, Cell Ranger, Seurat, or ACGT101), database versions, and filtering parameters in their final project reports. Software tool versions are documented in those reports. Because LC Sciences runs managed infrastructure, raw execution scripts, internal shell routines, and proprietary code (such as the ACGT101 codebase) are retained internally and not shared with clients.

What code and deliverables are provided for reproducibility?

Pepkio structures deliverables so your team can rerun or modify analyses locally. You receive executable R and Python code, parameter logs, version-pinned environment files, optional Nextflow or Snakemake scripts, and optional Docker or Conda container configurations.

LC Sciences delivers raw FASTQ files, aligned BAM files, variant VCF files, count tables, and structured HTML/PDF reports. They do not distribute custom executable pipeline code, shell scripts, or container recipes to clients.

How do they handle manuscript figures, Methods, and peer review?

Pepkio supplies high-resolution editable vector graphics (PDF, SVG) alongside R and Python plotting scripts, so you can change visual styling. Pepkio writes a manuscript-ready Methods section covering tools, parameters, and reference builds, and the lead bioinformatician can answer journal reviewer comments or run requested re-analyses.

LC Sciences includes publication-ready figures (heatmaps, volcano plots, PCA plots, GO/KEGG scatterplots) in PDF, PNG, and SVG within project reports. Reports contain structured methodology summaries and tool citations that authors can adapt into paper Methods sections. Technical support teams help clarify methodology or database parameters if journal reviewers raise questions after submission.

What are the turnaround times and project schedules?

LC Sciences quotes turnaround by assay type: about 20 business days post-QC for single-cell RNA-seq, 30 business days for shotgun metagenomics, 2 to 3 weeks for microarrays, 1 to 2 weeks for OligoMix synthesis, and 2 to 4 weeks for standard bulk RNA-seq.

Pepkio works on fixed dry-lab project schedules, typically delivering standard cohort analyses in 2 to 4 weeks and multi-contrast or custom multi-omics studies in 4 to 6 weeks. Those timelines include custom script tailoring, parameter sweeps, and verification.

How do client communication and analyst access work?

Pepkio pairs you with the senior computational biologist conducting your analysis. Communication is via email, phone, or video conference during scoping, execution, and manuscript preparation.

LC Sciences manages project communications primarily through assigned Project Managers who oversee sample receipt, wet-lab tracking, and report delivery. Bioinformatics scientists join scoping calls and post-delivery walkthroughs when custom technical consultation is needed.

How does pricing compare and what is included?

LC Sciences uses quote-based pricing per sample or per project, based on study design and sample volume. Base quotes cover sample QC, library prep, sequencing, standard bioinformatics processing (QC, alignment, differential expression, functional annotation), summary reports, and data delivery. Non-standard custom bioinformatics or multi-omics integrations are quoted separately.

Pepkio provides fixed-price quotes before work begins. Quotes cover data processing, script handover, editable vector figures, draft Methods text, and post-delivery reviewer support.

Who owns the data, code, and derived IP?

LC Sciences delivers raw FASTQ files, processed BAM/VCF files, count tables, and summary reports via secure cloud download links when the project is complete. Clients own their biological samples, raw sequencing data, and final derived output tables. LC Sciences retains ownership of its proprietary ACGT101 codebase and internal IP.

Pepkio transfers final output files, scripts, and documentation at project completion. Clients own the raw data, processed files, scripts, figures, and intellectual property.

How are custom or non-standard analyses handled?

Pepkio customizes R and Python scripts during scoping for non-standard experimental designs, custom reference genomes, or non-traditional statistical contrasts, and delivers the modified source code.

LC Sciences handles standard reference assemblies and established experimental protocols through automated pipelines. Non-standard workflows or advanced custom bioinformatics need specialized scoping and custom quote adjustments.

When Pepkio Is the Better Fit

• You already have raw FASTQ, BAM, VCF, or count files from a sequencing core and need dedicated dry-lab analysis.
• You require executable R and Python scripts, parameter logs, or container specifications to maintain local reproducibility.
• You want ongoing communication with the senior computational biologist executing your data analysis.
• You need editable vector figures (PDF/SVG) and a manuscript-ready Methods section drafted for journal submission.
• You want post-delivery technical support from the lead analyst for journal reviewer queries or requested re-analyses.

When LC Sciences Is the Better Fit

• You need a single US-based CRO to handle biological sample preparation, NGS sequencing, and bioinformatics reporting under one roof.
• Your project requires specialized RNA assays such as microRNA sequencing (miRNA-seq), degradome sequencing, circRNA-seq, or m6A RNA sequencing using their published ACGT101 pipeline.
• You require spatial transcriptomics (MERFISH, Stereo-seq, STARmap) or multi-omics assays including WGBS bisulfite sequencing, Olink proteomics, or LC-MS/MS metabolomics.
• You prefer managed CRO report deliverables (HTML/PDF summary reports and structured data tables) where pipeline execution is handled by the provider.
• You are submitting physical samples that require integrated library preparation and high-throughput sequencing hardware.

Frequently Asked Questions

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

Pepkio delivers executable R and Python scripts, command-line parameter logs, and optional Docker or Conda environment specs so your lab can inspect or rerun the analysis locally. LC Sciences operates a managed CRO model that delivers raw FASTQ files, processed count matrices, and HTML/PDF summary reports, but does not distribute internal pipeline scripts or proprietary source code such as ACGT101.

Will LC Sciences or Pepkio write the Methods section for my manuscript?

Pepkio includes a drafted, publication-ready Methods section covering reference assemblies, alignment tools, statistical cutoffs, and software packages used in your study. LC Sciences provides structured methodology text, algorithm descriptions, parameter settings, and software tool citations in the final project report, which authors can adapt into their manuscript.

How do both options handle journal Reviewer 2 comments during peer review?

Pepkio provides post-delivery technical support from the lead bioinformatician to help address reviewer queries or run requested re-analyses. LC Sciences offers technical support to clarify methodology descriptions, database builds, and parameter choices if journal reviewers ask after submission.

What if I already have raw FASTQ files and only need dry-lab bioinformatics?

Pepkio focuses on dry-lab analysis for existing FASTQ, BAM, or count files across transcriptomics, epigenomics, and genomics. LC Sciences is primarily an integrated wet-lab service provider, but they also accept raw FASTQ files, microarray data, or count matrices for standalone dry-lab re-analysis projects.

How long does an analysis take from data receipt to final deliverables?

Pepkio typically completes standard dry-lab cohorts in 2 to 4 weeks and complex multi-contrast studies in 4 to 6 weeks. LC Sciences quotes single-cell RNA-seq at about 20 business days post-QC, shotgun metagenomics at about 30 business days, microarrays at 2 to 3 weeks, and standard bulk RNA-seq at 2 to 4 weeks.

Can I rerun the pipeline on my university cluster or cloud infrastructure?

With Pepkio, you receive runnable R and Python code alongside version-pinned environment files or optional containers, so you can rerun the workflow on local servers. With LC Sciences, pipeline code runs on their internal computing infrastructure (300+ nodes), so workflows cannot be re-executed locally, though you receive all raw and processed data tables for downstream exploration.

Who will I communicate with if I need to adjust differential expression cutoffs?

With Pepkio, you communicate with the senior computational biologist who analyzed your dataset to refine parameters or rerun contrasts. With LC Sciences, your main point of contact is an assigned Project Manager who coordinates requests with internal technical teams, with technical specialists joining scoping or review calls when needed.

How does pricing compare between Pepkio and LC Sciences?

Pepkio provides upfront fixed-price quotes based on project scope, including data processing, script handover, vector figures, Methods text, and reviewer support. LC Sciences uses a quote-based model calculated per sample or per project based on wet-lab library prep, sequencing coverage, and dry-lab analysis specifications.

What happens if my study involves a non-model organism or custom reference genome?

Pepkio customizes R and Python workflows during initial project scoping for non-model genomes or custom reference assemblies, and hands over the modified code. LC Sciences supports non-model organisms across plants, animals, and microbes when a suitable reference genome assembly or transcript database is available.

What file formats are provided for publication figures?

Pepkio delivers high-resolution editable vector graphics (PDF, SVG) alongside R and Python plotting code, so you can control fonts, colors, and layout. LC Sciences provides publication-ready charts (heatmaps, volcano plots, PCA, GO/KEGG scatterplots) in vector (PDF, SVG) and raster (PNG) formats within their standard project deliverables.

How is raw sequencing data stored and archived after project completion?

LC Sciences delivers raw FASTQ files and processed outputs via secure cloud download links at project completion, and expects clients to download and archive their files promptly. Pepkio transfers all final output files, scripts, and documentation to the client at project completion for local archiving.

Do either LC Sciences or Pepkio require co-authorship on publications?

Neither LC Sciences nor Pepkio requires academic co-authorship for routine fee-for-service bioinformatics or sequencing. Standard academic practice is to acknowledge LC Sciences ("LC Sciences, Houston, TX") or Pepkio in your manuscript's Acknowledgments section.

Bottom Line

If your lab needs an integrated US wet-lab CRO for physical sample processing, NGS sequencing on NovaSeq or 10x Chromium platforms, and report delivery, especially for specialized microRNA, degradome, or m6A RNA assays, LC Sciences may be the better fit. If you already have raw sequencing files and want R and Python script delivery, collaboration with senior computational biologists, editable vector figures, and manuscript Methods writing, Pepkio may be the better fit.