Overview
We take raw sequencing reads to interpretable genomes: cleaned, assembled or aligned, annotated and checked. Short-read and long-read data are both supported, for microbes, plants, animals and humans.
Salient features
- Full read-to-variant pipelines with quality control at every step
- Short-read, long-read and hybrid workflows
- Annotated variant tables and publication-ready figures
Analyses we offer
WGS analysis
Calls SNVs, indels and structural variants from whole-genome data following best-practice pipelines.
Methods: gatk, deepvariant, nf-core sarek.
Genome annotation
Predicts genes and assigns functions to newly assembled prokaryotic or eukaryotic genomes.
Methods: prokka, bakta, BRAKER.
WES analysis
Calls and filters variants from exome capture data, for germline or somatic questions.
Methods: gatk, strelka, nf-core sarek.
De novo sequencing analysis
Assembles genomes without a reference from short or long reads, with polishing and scaffolding.
Methods: spades, canu, casanovo.
DNA fingerprinting
Genotypes short tandem repeats for identification, relatedness and repeat-expansion disorders.
Methods: HipSTR, GangSTR, ExpansionHunter.
aCGH data analysis
Detects copy-number gains and losses from array comparative genomic hybridisation.
Methods: DNAcopy, cnvkit, CGHcall.
SNP array data analysis
Processes SNP array intensities into genotypes and copy-number calls.
Methods: PennCNV, crlmm.
Tn-seq analysis
Identifies genes essential for growth from transposon insertion libraries.
Methods: transit.
Long-read sequencing analysis
Basecalls and analyses Oxford Nanopore and PacBio data, including alignment and variant calling.
Methods: dorado, minimap2, pbmm2.
Structural variant calling
Detects deletions, duplications, inversions and translocations from short or long reads.
Methods: Sniffles, manta, delly.
Copy number variation (CNV) analysis
Estimates copy number across the genome from sequencing depth.
Methods: cnvkit, CNVnator.
Variant annotation & interpretation
Annotates variants with gene impact, population frequency and clinical databases.
Methods: ensembl-vep, SnpEff.
Genome assembly quality control
Assesses completeness, contiguity and correctness of genome assemblies.
Methods: quast, merqury.
Sequencing read QC & trimming
Checks read quality, removes adapters and low-quality bases, and summarises runs across samples.
Methods: FastQC, MultiQC, fastp.
Pangenome analysis
Defines core and accessory genes across many genomes and builds graph pangenomes.
Methods: panaroo, Roary, pggb.
What you receive
- A written report with methods, parameters and interpretation
- Processed data tables and publication-quality figures
- Scripts and settings so every result can be reproduced
Not sure which analysis fits your data? Contact us and we will advise.