Bioinformatics services
Complete analysis of already-sequenced NGS data. Agnostic platform: we work with FASTQ from Illumina, DNBSEQ, Oxford Nanopore or PacBio. Deliverables ready for publication or clinical use.
What we offer
From a basic alignment to an ACMG/AMP clinical report. You build your service à la carte according to your needs.
Alignment
BWA-MEM2 or minimap2 (long reads) against GRCh38/T2T. Sorted, deduplicated and with optional BQSR.
BAM / CRAMVariant calling
DeepVariant or GATK4 for germline. Strelka/Mutect2 for somatic. Manta + CNVkit for SV/CNV.
VCF · SNV · Indels · SVACMG annotation
VEP + ClinVar + gnomAD + OMIM + HPO + SpliceAI. Automatic and reviewed ACMG/AMP classification.
Annotated VCF + TSVRNA-seq
STAR + Salmon/featureCounts. DESeq2/edgeR for differential expression. GSEA, heatmaps and volcanoes.
Counts · DEG · GSEAMetagenomics
16S (DADA2/QIIME2) or shotgun (MetaPhlAn4, HUMAnN3). Alpha/beta diversity, taxonomy and functionality.
ASV · Kraken · PathwaysClinical reports
ACMG/AMP report signed by a qualified professional, with recommendations, segregation and bibliographic references.
PDF + editable ODTValidated pipelines
All our analyses run on nextflow/Snakemake pipelines with version control, reproducible containers and validation against reference datasets (GIAB HG002/HG003/HG004).
- WGS germlineBWA-MEM2 → DeepVariant/GATK4 → VEP → ACMG. Validated with GIAB, F1 > 0.99 in SNV.
- WES germlineTwist/IDT capture → adapted WGS pipeline → panel filters. Mean coverage >100x.
- Somatic WGSStrelka2 + Mutect2 with matched normal. Optional TMB, MSI and mutational signatures.
- RNA-seqSTAR 2-pass + Salmon quant. DESeq2 with apeglm shrinkage. Interactive HTML reports.
- 16S ampliconDADA2 → QIIME2 → SILVA 138 taxonomy. ASVs with species-level resolution.
- Shotgun metagenomicsMetaPhlAn4 + HUMAnN3. MetaCyc pathways, enzymes and resistance genes (CARD).
What kind of data do we analyse?
Platform and chemistry agnostic. Send us your FASTQ and we take care of the rest.
WGS
Whole genomes 15x–60x. Human, mammals, plants, bacteria. Short read and long read.
WES
Exomes 50x–200x with any commercial capture (Twist, Agilent, IDT, Roche, MGI).
Panels
Targeted panels >500x, UMI optional. Any commercial or custom design.
RNA-seq
mRNA, total RNA, small RNA, stranded/unstranded, single-end or paired-end.
16S amplicon
V3-V4 or full length (PacBio). DADA2/QIIME2 analysis with SILVA taxonomy.
Shotgun
Complete metagenomics, taxonomy and functionality. Antimicrobial resistance.
Long read
Oxford Nanopore or PacBio HiFi. SV, phasing and methylation. Optional de novo assembly.
Custom
Another data type? Ask us.
What you receive
Standard formats ready to publish, share or load onto your platform. Reproducible scripts and full documentation included.
- Indexed BAM/CRAMReferenced to GRCh38 (or T2T on request), with full metadata.
- Annotated VCFIn VCF 4.3 format, VEP multi-consequence annotation, compatible with any platform.
- TSV/CSV tablesFilterable listings with ACMG classification, frequencies and in silico scores.
- HTML reportsQC (MultiQC), DEG results (iSEE), metagenomics (fastp, Krona). Interactive.
- Clinical PDF reportWhen applicable, signed by our responsible professional.
- Scripts and documentationComplete Nextflow/Snakemake runs, exact tool versions and references.
Methylation arrays
EPIC v2 · EPIC v1 · 450K · 27K
Quality control and normalization of methylation data (sesame) with a per-sample quality report. 18 €/sample.
Extensions in preparation (DKFZ brain-tumour classifier, methylation clocks): ask about availability.
Host–microbiome integration
MaAsLin2 · multi-omic integration (DIABLO)
Statistical association between microbiome gene families and clinical phenotype or metadata (multivariable mixed models), with optional multi-omic integration. Ideal for cohorts with microbiome data plus clinical, metabolomic or transcriptomic data.
€136 per project (up to 30 samples) · additional samples €4/sample.
Technical research report (RUO). Internal validation: pipeline verified with known signal (5/5 recovered).
Population genomics, epigenomics and neoantigens
GWAS — genome-wide association studies
Genotype QC and population-structure control (PCs) with PLINK2, and association testing with regenie (quantitative or binary traits, covariates). From 200 €/project (≤200 samples).
Epigenomics — ATAC-seq, ChIP-seq and WGBS
Chromatin peak calling with MACS3 (narrow/broad) and DNA methylation profiling by WGBS with Bismark. From 36 €/sample (peaks) · from 120 €/sample (WGBS).
Neoantigens — HLA binding prediction
Peptide–HLA (class I) binding prediction with an open-source predictor and prioritisation by agretopicity, from your somatic variants and HLA alleles. From 320 €/sample.
Is your data waiting for analysis?
Tell us what you have and what you need. We send you a quote and estimated time within 48 h. For large datasets (FASTQ/BAM) we send a secure SFTP link after your request; for small files, web upload.