NGS Data Analysis. Raw Reads → Results. Publication-Ready.

Upload your FASTQ, BAM, or VCF files. Get QC, alignment, quantification, differential expression, variant calling, pathway analysis, and publication-ready figures — in 3–7 days.

Get Free Quote → See All Assay Types

$150

Per Sample
Starting

3–7d

Turnaround
Time

Assay Types
Supported

PhD

Expert
Review

How It Works

Your Data Through Our Pipeline

Every sample goes through a validated, reproducible bioinformatics workflow — the same tools used by top-tier research institutions.

Upload

FASTQ · BAM · VCF · CRAM via SFTP or cloud link

→

QC

FastQC · MultiQC · adapter trimming · quality filtering

→

Alignment

BWA-MEM2 · STAR · HISAT2 · Minimap2 · Bowtie2

→

Quantification

featureCounts · Salmon · RSEM · GATK HaplotypeCaller

→

Analysis

DE · pathway · GO · clustering · variant annotation

→

Deliver

Report · figures · methods · raw files · reproducible code

7 Assay Types

Every NGS Assay. One Team.

Whatever your sequencer produced — Illumina, BGI, ONT, PacBio — we analyze it. Click any assay for full details.

Most Requested

Bulk RNA-Seq Analysis

$150–300/sample

Differential gene expression, pathway enrichment (KEGG, GO, Reactome), gene set enrichment analysis (GSEA), heatmaps, volcano plots, PCA. Supports any reference organism.

QC report (FastQC + MultiQC)

Normalized count matrix

DE gene list (padj < 0.05)

Pathway & GO enrichment

Volcano, MA, heatmap plots

PCA & sample clustering

Methods section (copy-paste)

Reproducible R/Python code

STAR Salmon DESeq2 edgeR clusterProfiler

TAT: 3–5 days

WGS / WES Variant Analysis

$200–500/sample

Germline or somatic variant calling, annotation (ClinVar, gnomAD, dbSNP, COSMIC), filtering, ACMG classification, copy number variation, structural variants. Human, mouse, or any reference genome.

Variant calling (SNV + InDel)

Annotated VCF file

ClinVar / gnomAD annotation

ACMG pathogenicity classification

CNV detection

Coverage & QC statistics

Filtered variant report

IGV screenshots (key variants)

BWA-MEM2 GATK DeepVariant ANNOVAR VEP

TAT: 5–7 days

Premium

Single-Cell RNA-Seq

$400–800/sample

10x Genomics, Drop-Seq, Smart-Seq2. Cell-type clustering, marker gene identification, trajectory analysis, cell-cell communication, integration across samples/conditions.

QC & doublet removal

UMAP / t-SNE visualizations

Cell type annotation

Marker gene tables per cluster

DE between conditions

Trajectory / pseudotime

CellChat / ligand-receptor

Multi-sample integration

CellRanger Seurat Scanpy scVI

TAT: 7–10 days

Metagenomics (16S / Shotgun)

$150–250/sample

16S rRNA amplicon or whole-genome shotgun sequencing. Taxonomic profiling, alpha/beta diversity, differential abundance, functional prediction (PICRUSt2, HUMAnN3). Gut, soil, water, clinical — any microbiome.

OTU/ASV tables

Taxonomic bar plots

Alpha diversity (Shannon, Chao1)

Beta diversity (PCoA, NMDS)

Differential abundance (LEfSe)

Functional prediction

Phylogenetic trees

Statistical comparisons

QIIME2 DADA2 Kraken2 MetaPhlAn

TAT: 3–5 days

ChIP-Seq / CUT&RUN

$200–400/sample

Peak calling, motif analysis, differential binding, annotation of peaks to nearest genes, signal heatmaps, genome browser tracks. Histone marks and transcription factors.

Peak calling (MACS2)

Motif enrichment (HOMER)

Peak annotation (TSS, enhancers)

Differential binding analysis

Signal heatmaps & profiles

BigWig genome browser tracks

MACS2 HOMER DiffBind deepTools

TAT: 5–7 days

ATAC-Seq

$200–400/sample

Open chromatin profiling. Peak calling, nucleosome-free region identification, TF footprinting, differential accessibility between conditions, integration with RNA-Seq.

Open chromatin peaks

TSS enrichment plots

TF motif footprinting

Differential accessibility

Fragment size distribution

Integration with expression data

MACS2 Genrich chromVAR ArchR

TAT: 5–7 days

Multi-Omics Integration

Combine RNA-Seq + ATAC-Seq + ChIP-Seq + WGS for a complete picture. We integrate across data modalities with statistical rigor — from joint NMF to MOFA+ to custom correlation frameworks. Starting at $5,000 per project.

Discuss Multi-Omics Project →

Pricing

Transparent Per-Sample Pricing

All prices in USD. Volume discounts for 20+ samples. Custom quotes for complex or multi-phase projects.

Assay Type	Per Sample	10+ Samples	50+ Samples	TAT	Input
Bulk RNA-Seq	$200	$170	$150	3–5 days	FASTQ (PE/SE)
WES (Exome)	$250	$220	$200	3–5 days	FASTQ / BAM
WGS (30x)	$400	$350	$300	5–7 days	FASTQ / CRAM
scRNA-Seq (10x)	$600	$500	$400	7–10 days	FASTQ / CellRanger
16S Metagenomics	$150	$130	$110	3–5 days	FASTQ (PE)
Shotgun Metagenomics	$250	$220	$190	5–7 days	FASTQ (PE)
ChIP-Seq / CUT&RUN	$300	$260	$220	5–7 days	FASTQ (PE)
ATAC-Seq	$300	$260	$220	5–7 days	FASTQ (PE)

What's Included

QC, alignment, primary + secondary analysis, publication-ready figures, methods section, raw analysis files, one round of revision. All tools and compute costs included.

Add-Ons

Rush delivery (48hr): +50%. Additional comparisons: $200 each. Custom visualization: $300–$800. Manuscript figure polishing: $500. GSEA deep-dive: $400.

Volume & Retainer

100+ samples: custom quote. Monthly retainer (10 samples/mo): 25% off list. Annual contracts: 30% off + priority queue. Academic pricing available.

Any Sequencer. Any Format.

We're platform-agnostic. Whether your data comes from Illumina NovaSeq, BGI DNBSEQ, Oxford Nanopore, PacBio, or Ion Torrent — we handle it. Upload via SFTP, S3, Google Drive, or any cloud link.

Input Formats

FASTQ BAM CRAM VCF FASTA SRA

Output Formats

PDF Report CSV/TSV VCF R/Py Code Figures BAM/BigWig

Sequencer Compatibility

Illumina

NovaSeq · HiSeq · MiSeq · NextSeq · iSeq

BGI / MGI

DNBSEQ-G400 · DNBSEQ-T7 · MGISEQ-2000

Oxford Nanopore

MinION · GridION · PromethION

PacBio

Sequel II/IIe · Revio · Vega

FAQ

Frequently Asked Questions

What data do I need to send you?

Raw sequencing files (FASTQ is preferred), a sample sheet mapping filenames to conditions/groups, and the reference organism. If you have BAM, VCF, or count matrices from a previous analysis, we can work with those too. We'll request any missing info during our free consultation call.

How do I transfer large sequencing files?

We support SFTP, AWS S3, Google Cloud Storage, Google Drive, Dropbox, BaseSpace, or SRA accession numbers. For SFTP, we provide a private server with credentials. For cloud, share a link. We handle all the download and organization — just point us at the data.

Do you work with non-human organisms?

Yes — we work with any organism that has a reference genome or transcriptome. Human, mouse, rat, zebrafish, Arabidopsis, rice, bacteria, fungi, viruses — you name it. For non-model organisms, we can do de novo assembly or align to the closest available reference.

Is my data confidential?

Absolutely. We sign an NDA before any data transfer. Your data is stored on encrypted servers, accessed only by assigned analysts, and deleted upon project completion (or retained for a defined period if you prefer). You retain 100% ownership of all results, code, and deliverables. No authorship requirements.

Can I request revisions?

One round of revisions is included in the price. We share interim results for feedback before final delivery, so major rework is rare. Additional revisions or scope changes are quoted transparently — no surprises.

Can you help write the methods section for my paper?

Yes — every standard analysis includes a copy-paste-ready methods section describing tools, versions, parameters, and statistical tests used. This is journal-ready (we follow Nature/Cell/Science formatting conventions). If you need help with the results narrative or figure legends, that's available as an add-on.

What if I just have a VCF and need interpretation, not raw data processing?

We handle that too. Upload your VCF, and we annotate, filter, classify (ACMG), and deliver an interpretation report. For clinical-grade interpretation, ask about our Genix Clinical Genomics platform — it's purpose-built for this with South Asian population frequency integration.

Do you offer academic / student discounts?

Yes. Academic pricing is available — contact us with your institutional email. PhD students and postdocs get additional flexibility on payment terms. We've been in your shoes — we want to make computational biology accessible.

Get Started

Send Us Your Data.
Get Results in Days.

Free consultation. Clear quote within 24 hours. No obligation. We'll tell you exactly what we'll deliver, when, and for how much.

Email

biocompute@genix.ai

Response Time

Within 24 hours, typically same day

Why researchers choose us :

✓PhD founder reviews every deliverable — not a junior analyst

✓50–70% lower cost than Tradition bioinformatics CROs

✓Publication-ready figures you can drop straight into your manuscript

✓Full NDA, IP ownership, data deletion on request

✓We write the methods section — you just copy-paste

Request NGS Analysis Quote

Name *

Email *

Organization

Assay Type

Number of Samples

Organism

Project Details

Quote within 24 hours. No spam, no obligation.

Need More Than NGS Analysis?

Explore our full bioinformatics service portfolio.

🧬

Platform

BioCompute

Technology

Solutions

Company

Compliance

Security Architecture

Legal

Connect

Developed in Association with Chadura.

NGS Data Analysis. Raw Reads → Results. Publication-Ready.

Your Data Through Our Pipeline

Upload

QC

Alignment

Quantification

Analysis

Deliver

Every NGS Assay. One Team.

Bulk RNA-Seq Analysis

WGS / WES Variant Analysis

Single-Cell RNA-Seq

Metagenomics (16S / Shotgun)

ChIP-Seq / CUT&RUN

ATAC-Seq

Multi-Omics Integration

Transparent Per-Sample Pricing

What's Included

Add-Ons

Volume & Retainer

Any Sequencer. Any Format.

Input Formats

Output Formats

Sequencer Compatibility

Illumina

BGI / MGI

Oxford Nanopore

PacBio

Frequently Asked Questions

What data do I need to send you?

How do I transfer large sequencing files?

Do you work with non-human organisms?

Is my data confidential?

Can I request revisions?

Can you help write the methods section for my paper?

What if I just have a VCF and need interpretation, not raw data processing?

Do you offer academic / student discounts?

Send Us Your Data. Get Results in Days.

Email

Response Time

Why researchers choose us :

Request NGS Analysis Quote

Need More Than NGS Analysis?

Protein Modeling & Docking

Pipeline Engineering

All Services

Platform

BioCompute

Technology

Solutions

Company

Compliance

Legal

Connect

Send Us Your Data.
Get Results in Days.