What We Offer
Ready-to-Run Pipelines
Custom Analytics
Tailored Analyses to Empower Your Research
When off-the-shelf solutions fall short, our custom analytics services step in. We work closely with you to design and implement bespoke analyses that align with your research goals, clinical needs, or product development. Whether you are integrating multi-omic data, fine-tuning statistical models, or surfacing actionable insights from complex data, we deliver rigorously validated results with clear, decision-ready interpretation. Your questions are unique—your analytics should be too. -
Constultations
Fast, Reliable, and Fully Reproducible
Choose from a suite of fully-automated, production-tested pipelines designed to deliver high-quality results with minimal setup. Every workflow is optimized for speed and accuracy, providing standard outputs for all sequencing applications—without the need to build from scratch. Whatever you are analyzing, our pipelines are built to scale with your data and deliver publication-ready outputs.
VIEW PRICING & DETAILS
Expert Guidance to Showcase Your Science
From study design to final figures, our consultations provide the strategic insight and technical expertise you need at every step. We help you navigate complex data, select the right analytical tools, and communicate your findings with clarity and impact. Good bioinformatics starts with the right questions- our consults are built to clarify your goals and point you toward the most efficient and insightful analysis possible—whether that means a full project, a pipeline, or just some sound advice.
Pipelines
Data Pre-processing
Transform your raw sequencing data into ready-to-analyze outputs. Rest assured that we can handle all major NGS platforms including Illumina, PacBio, and Oxford Nanopore. Whatever your end point, you can't go wrong by starting here.
- Input: Raw Sequencing Data (bam, fastq, vcf, etc.)
- Output: Merged, Aligned, Sorted, & Indexed Data
Small (<10 GB): $69/sample
Large (>10 GB): $99/sample
Data Pre-processing
From data tidying to comparative statistical testing and visualization, this pipeline ensures your data is ready for whatever comes next.
- Processing Steps Include:
- Read trimming (optional)
- Merging (by sample)
- Aligning (desired reference)
- Sorting
- Indexing
- Summary Statistics Report Includes:
- Total passed & failed reads
- Total passed & failed bases
- Percent alignment to reference
Ideal For: Researchers and clinicians needing to prepare raw data for any downstream analysis.
NGS Summary Statistics
Gain an in-depth understanding of your sequencing data with key insights into total and per sample outputs, pass & fail rates, read lengths, alignment, and a number of platform specific metrics. Sequencing data is big, start dissecting it here.
- Input: Aligned or Raw Data & Reference (bam, fastq, vcf, etc.)
- Output: Passed/Failed Reads, Mean Read Length/N50, Quality Scores,
Genome Coverage, Alignment Rate, & Platform-Specific Metrics
Pricing
Small (<10 GB): $39/sample
Large (>10 GB): $69/sample
NGS Summary Statistics
See your sequencing data with unparalleled clarity. Powerful insights don't have to be complex. In fact, here, we think the simpler the better.
- Universal Summary Metrics:
- Total Passed/Failed Reads & Bases with Failure Rate
- Read Length Distribution & N50
- Q-Score Distrubtion & Quality Summary Statistics
- Whole-genome and Region-specific Alignment Rates
- % Adapter Content
- Platform-specific Summary Metrics:
- Illumina – Per-base N content, Overrepresented Sequences, Tile/Lane QC
- ONT – Initial/Final Pore Counts, Channel Activity, & Signal-derived QC
- PacBio – Read Type Classification (HiFi/CCS vs CLR), Polymerase/Subread Lengths,
ZMW Pass Counts, and Insert Size Distribution
Ideal For: This pipeline is ideal for anyone needing a quick, yet comprehensive, quality assessment of their sequencing data.
RNA-Seq
Unlock the secrets of gene expression with our comprehensive RNA-Seq pipeline. We deliver key quality metrics and quantification for every gene, so you can confidently move to differential expression analysis. Start gaining valuable insights from your transcriptome here.
- Input: Raw Sequencing Data (bam or fastq) & Reference(s)
- Output: Percent rRNA Contamination, Mapping Rates, Duplicate Read Counts,
Expression Profiling, & Differential Expression
Small (<10 GB): $129/sample
Large (>10 GB): $159/sample
RNA-Seq
Transform raw data with a complete transcriptome analysis complete with gene expression tables- ready for downstream interpretation.
- Quality Control Metrics:
- Percent rRNA contamination
- Read mapping & duplicate read rates
- Expression Profiling:
- Gene- and transcript-level quantification (TPM/FPKM)
- Raw and normalized count matrices
- Differential Expression:
- Statistical summary & gene expression tables
Ideal For: General RNA characterization and identifying changes in gene expression across different biological conditions.
Metagenomics
Uncover the microbial composition of your samples with our metagenomics pipeline. We quantify species-level abundance and provide robust taxonomic classification, making it easy to identify pathogens and track contamination. Start exploring new microbial worlds here.
- Input: Raw Sequencing Data (bam or fastq) & Reference(s)
- Output: Total Reads & Bases by Species, Abundance –
Actual and Theoretical (if applicable)
Small (<10 GB): $169/sample
Large (>10 GB): $199/sample
Metagenomics
Metagenomic deconvolution can be a daunting task. Rest assured, this pipeline's robust capacity provides in-depth technical details on the species abundance and taxonomy of your data.
- Key Features:
- Reference-based Mapping with Automatic Index Generation
- Custom Alignment Options from 16s/18s/ITS to Whole-genome
- Alignment Filtering by Orientation and Mapped Read Status
- Customizable Accession-to-species Mapping
- Deliverables:
- Per-barcode .aln.bam files of mapped reads
- Final summary table including:
- Barcodes/Sample IDs
- Aligned Read & Base Counts
- % Abundance
Ideal For: This pipeline is ideal for identifying and quantifying microbial species within a sample, particularly for pathogen detection and environmental studies.
Native Modifications
Dive deep into epigenetics with our native modifications pipeline, detecting DNA modifications directly from ONT data without chemical conversion. We deliver per-base modification probabilities for 5mC, 5hmC, and 6mA, giving you unprecedented insight into epigenetic marks. Start your journey into epigenetic profiling here.
- Input: Aligned Sequencing Data (ONT)
- Output: Modification Probabilities-
5mC, 5hmC & 6mA (calls.tsv)
Small (<10 GB): $99/sample
Large (>10 GB): $129/sample
Native Modifications
This ONT-specific pipeline enables the detection of native DNA modifications without the need for chemical treatment or bisulfite conversion. It uses aligned ONT sequencing data to compute per-base modification probabilities, providing direct insight into epigenetic marks.
- Key Features:
- Aligned Oxford Nanopore Data (Basecalling ON)
- Supports Fast, HAC, & SUP ONT Basecalling Models
- High Accuracy Model Achieves over 95% Accuracy for 5mC Detection
- Deliverables:
- Residue-level Call Probabilites (calls.tsv) for:
- 5-methylcytosine (5mC)
- 5-hydroxymethylcytosine (5hmC)
- 6-methyladenine (6mA)
Ideal For: Native epigenetic profiling in research and clinical genomics workflows using long-read sequencing.
Methylation Profiling & Differential Methylation
Pinpoint crucial epigenetic changes with our methylation pipeline. We quantify DNA methylation at single-base resolution and identify differentially methylated regions (DMRs) between sample groups, providing clarity on regulatory dynamics. Characterizing novel epigenetic profiles and biomarkers starts here.
- Input: Aligned ONT (appropriate basecalling) or BS-Seq Data
- Output: Per-CpG Methylation Frequency & Global & Regional Summaries (.calls.tsv).
Optional Differential Methylation Add-on (.csv)
Small (<10 GB): $219/sample
Large (>10 GB): $249/sample
Methylation Profiling & Differential Methylation
Our robust workflow quantifies DNA methylation at single-base resolution. Identify key differences in regulatory elements and between sample groups, easier than ever before.
- Multi-platform Compatability:
- Sequencing–
- ONT Native Read Sequencing (Basecalling ON)
- Bisulfite-Seq (WGBS, RRBS) or EM-Seq
- MeDIP-seq
- Methylation Microarray–
- .idat and sentrix files
- Differential Methylation–
- Sequencing Data, Modification Tags (calls.tsv) files, or Methylation Microarray (idat) files
- Sample Group Definitions (metadata)
- Sequencing–
- Output:
- Per-base/probe methylation frequencies (5mC/5hmC)
- Statistical Summary Tables per Gene, CpG Island, or DMR
- Optional region-level output in BED or bigWig format for browser visualization
Ideal For: Novel epigenetic biomarker discovery, understanding regulatory dynamics, or comparing methylation landscapes across different conditions.