Bioinformatics · NGS Analysis

From Raw Reads to
Biological Insights

Comprehensive downstream bioinformatics analysis for every NGS application, delivered as publication-ready reports with full reproducibility.

🧬 RNA-seq 🔬 WGS / WES 🦠 Metagenomics 🔗 Single-Cell 🌿 Epigenomics ⚙️ Custom Pipelines
7+
Analysis Categories
50+
Distinct Services
100%
Reproducible Pipelines
24/7
Expert Support

Our Services

Full-Spectrum NGS Bioinformatics

Whether you need standard analysis or a fully bespoke pipeline, our team of bioinformaticians delivers accurate, reproducible, and interpretable results.

🧬
RNA-seq & Transcriptomics
mRNA · lncRNA · circRNA · Small RNA · Isoform · Long-Read
Get Quote →
Differential Gene Expression
Quantify transcript abundance and identify statistically significant differentially expressed genes between conditions.
DESeq2edgeRlimma
Pathway & GO Enrichment
Gene Ontology (GO) annotation and KEGG pathway mapping to place DEGs in biological context.
KEGGGOGSEA
Alternative Splicing Analysis
Detection of differential splicing events, exon skipping, intron retention, alternative 5'/3' splice sites.
rMATSSTARStringTie
Fusion Gene Discovery
Identify chimeric transcripts and gene fusions, commonly applied in cancer transcriptomics and oncology research.
STAR-FusionARRIBA
Novel Transcript Annotation
Discover and annotate previously unannotated transcripts including novel lncRNAs and isoforms.
StringTieCufflinks
Small RNA / miRNA Analysis
Profiling of microRNAs, piRNAs, and other small non-coding RNAs with differential expression and target prediction.
miRDeep2miRBase
lncRNA & circRNA Analysis
Identification, quantification, and functional annotation of long non-coding and circular RNA species.
CIRCexplorerfind_circ
Long-Read Isoform Sequencing
Full-length isoform characterization using PacBio Iso-Seq or Oxford Nanopore direct cDNA sequencing.
PacBio Iso-SeqNanopore
🔬
Whole Genome & Exome Sequencing Analysis
SNP · InDel · CNV · SV · Variant Annotation · Population Genomics
Get Quote →
SNP & InDel Calling
Accurate detection of single nucleotide polymorphisms and small insertions/deletions from germline or somatic samples.
GATKDeepVariantFreeBayes
Structural Variant (SV) Detection
Identification of large-scale genomic rearrangements: deletions, duplications, inversions, translocations, and novel insertions.
MantaDELLYSVABA
Copy Number Variation (CNV)
Genome-wide CNV detection and visualization, essential for cancer genomics, rare disease, and population studies.
CNVkitGATK gCNV
Somatic Mutation Analysis
Tumor–normal paired analysis for somatic SNVs, InDels, SVs, and mutational signature profiling in cancer samples.
Mutect2Strelka2SigProfiler
Variant Annotation & Filtering
Functional annotation of variants against ClinVar, dbSNP, gnomAD, and custom databases with pathogenicity scoring.
ANNOVARVEPSnpEff
Population Genomics & GWAS
Principal component analysis, admixture, linkage disequilibrium, and genome-wide association studies across cohorts.
PLINKADMIXTUREGCTA
Pharmacogenomics (PGx)
Identification of clinically relevant pharmacogenomic variants affecting drug metabolism (CYP genes, transporter genes).
PharmGKBCPIC
Low-Pass WGS Analysis
Cost-effective genome-wide variant discovery using statistical imputation from low-coverage (1–4×) sequencing data.
GLIMPSEimputation
🦠
Metagenomics & Microbiome Analysis
16S · 18S · ITS · Shotgun Metagenomics · Functional Profiling
Get Quote →
16S rRNA Amplicon Analysis
OTU/ASV clustering, taxonomic classification, and alpha/beta diversity metrics for bacterial community profiling.
QIIME2DADA2SILVA
18S & ITS Amplicon Analysis
Eukaryotic and fungal community profiling using 18S rRNA and ITS1/ITS2 amplicon sequencing with standard databases.
QIIME2UNITEPR2
Shotgun Metagenomics
Culture-independent whole-community profiling: species composition, relative abundance, and resistome analysis.
Kraken2MetaPhlAnBracken
Functional Metagenomics (HUMAnN)
Metabolic pathway and gene family abundance profiling from metagenomic reads using UniRef and MetaCyc databases.
HUMAnN3MetaCycKEGG
Microbial Diversity Analysis
Alpha diversity (Shannon, Chao1, Simpson), beta diversity (UniFrac, Bray-Curtis), and statistical group comparisons.
veganphyloseq
Metagenome-Assembled Genomes (MAGs)
Reconstruction and quality assessment of individual microbial genomes from complex metagenomic samples.
MetaBAT2CheckMGTDB-Tk
🌿
Epigenomics Analysis
ChIP-seq · ATAC-seq · WGBS · CUT&RUN · CUT&TAG
Get Quote →
ChIP-seq Analysis
Peak calling for histone modifications and transcription factor binding, followed by motif enrichment and annotation.
MACS2/3HOMERdeepTools
ATAC-seq Analysis
Open chromatin profiling with peak calling, nucleosome positioning, footprinting, and differential accessibility analysis.
ATAC-seqTOBIASMACS2
CUT&RUN / CUT&TAG Analysis
High-resolution protein–DNA interaction mapping with lower background and less starting material than ChIP-seq.
Bowtie2SEACRMACS2
Whole-Genome Bisulfite Sequencing (WGBS)
Base-resolution DNA methylation quantification across the entire genome, including CpG island analysis and DMR detection.
BismarkMethylKitDSS
Reduced Representation Bisulfite Sequencing (RRBS)
Cost-effective CpG methylation profiling enriched at CpG-dense regions, ideal for large cohort epigenetic studies.
BismarkRnBeads
TF Motif Discovery
De novo and known transcription factor motif enrichment analysis within open chromatin or ChIP-seq peak regions.
HOMERMEME-ChIPJASPAR
🔗
Single-Cell & Spatial Analysis
scRNA-seq · scATAC-seq · Spatial Transcriptomics · Multi-omics
Get Quote →
scRNA-seq: Cell Clustering & Annotation
Dimensionality reduction (PCA, UMAP, t-SNE), unsupervised clustering, marker gene identification, and cell type annotation.
SeuratScanpyscVI
Differential Expression (Single-Cell)
Pseudobulk and single-cell level DEG analysis between conditions, time points, or cell populations with multiple testing correction.
DESeq2WilcoxonMAST
Trajectory & Pseudotime Analysis
Reconstruct cellular differentiation pathways and developmental trajectories from snapshot single-cell data.
Monocle3RNA velocity
Cell–Cell Communication
Ligand–receptor interaction inference between cell types to map intercellular signaling networks from scRNA-seq data.
CellChatNicheNetLIANA
scATAC-seq Analysis
Single-cell chromatin accessibility profiling with peak-level clustering, cell type annotation, and gene activity scoring.
ArchRSignacSnapATAC2
Spatial Transcriptomics Analysis
Mapping gene expression to tissue architecture from Visium, Stereo-seq, or MERFISH data with spatial deconvolution.
SeuratSquidpyBayesSpace
Multi-omics Integration (Single-Cell)
Joint analysis of scRNA-seq + scATAC-seq (CITE-seq, 10x Multiome) for linked transcriptomic and epigenomic profiling.
WNNMOFA+Seurat
TCR / BCR Repertoire Analysis
V(D)J clonotype reconstruction and repertoire diversity from single-cell immune profiling (10x Genomics Immune Profiling).
ScirpyImmunarchVDJtools
🧩
De Novo Assembly & Genome Annotation
Short-Read · Long-Read · Hybrid · Chromosome-Level · Annotation
Get Quote →
Short-Read De Novo Assembly
Illumina-based genome assembly for bacteria, fungi, and small eukaryotes with contig-level or scaffold-level output.
SPAdesVelvetABySS
Long-Read Assembly (T2T)
Chromosome-scale, telomere-to-telomere assembly using PacBio HiFi or Oxford Nanopore ultralong reads.
HifiasmFlyeNextDenovo
Hybrid Assembly
Combining the accuracy of Illumina short reads with the contiguity of long reads for high-quality genome drafts.
UnicyclerHybracter
Structural & Functional Annotation
Gene prediction, repeat masking, non-coding RNA annotation, and functional annotation against public databases.
BRAKER3RepeatMaskereggNOG
Comparative Genomics
Synteny analysis, pan-genome construction, ortholog clustering, and phylogenomics across multiple genomes.
OrthoFinderMCScanBUSCO
Metagenome Assembly
Assembly of complex environmental and clinical metagenomic samples into contigs, followed by binning into MAGs.
MEGAHITmetaSPAdesMetaBAT2
⚙️
Custom Pipeline Development
Bespoke Analysis · Multi-omics Integration · Cloud · Automation
What We Build
  • End-to-end automated NGS pipelines (FASTQ → report)
  • Multi-omics integration (genomics + transcriptomics + epigenomics)
  • Clinical variant interpretation pipelines
  • Custom database creation and querying
  • Regulatory-compliant validation (IVD/clinical-grade)
  • Cloud-native Nextflow / Snakemake workflows
  • Interactive R Shiny or Python Dash dashboards
Standard Deliverables
  • QC metrics and multiqc HTML report
  • Processed count matrices / VCF files
  • Publication-ready figures (volcano, heatmap, UMAP)
  • Detailed methods section for manuscripts
  • Reproducible code repository (GitHub)
  • Interpreted biological summary report
  • Raw + processed data via secure portal

Our Stack

Industry-Standard Tools & Databases

Every pipeline we build uses validated, peer-reviewed tools, ensuring reproducibility and publication acceptance.

Step Purpose Tools We Use
QC & Trimming Adapter removal, quality filtering, read statistics FastQC MultiQC Trim Galore fastp
Alignment Reference-based mapping for short and long reads STAR BWA-MEM2 Bowtie2 minimap2
Quantification Gene/transcript count estimation Salmon featureCounts HTSeq kallisto
Variant Calling SNP, InDel, SV, CNV detection GATK4 Mutect2 DeepVariant Manta
Annotation Variant and gene functional annotation ANNOVAR VEP SnpEff eggNOG-mapper
Statistics Differential analysis and enrichment testing DESeq2 edgeR clusterProfiler fgsea
Single-Cell scRNA-seq and scATAC-seq analysis Seurat v5 Scanpy ArchR Monocle3
Visualization Plots, figures, and interactive reports ggplot2 matplotlib IGV R Shiny
Workflow Pipeline orchestration and reproducibility Nextflow Snakemake Docker Conda

Get Started

Ready to analyze your data?

Tell us your experimental design and we'll propose the right analysis pipeline, from a simple DGE analysis to a full multi-omics integration project.

Compare 5 providers → ← Back to Services

Or email us at info@quickseq.bio

QuickSeq
Services Process Why Us About Us 👤 Sign In Contact