Science · Methods & Publications

Methods, tools & published work

Tool selection follows community benchmarks and peer-reviewed comparisons — not vendor relationships. Each tool listed here is in active use in project delivery. Where multiple tools address the same problem, the choice is documented in project methods sections.

Benchmark-guided selection

Tools are evaluated against independent benchmarks (GIAB for variant calling, DREAM challenge for somatic, PBMC datasets for single-cell) before adoption.

Explicit version pinning

Every analysis records exact software versions in environment.yml or container image digests. Results are labelled with the pipeline version that produced them.

Methods written to publication standard

Delivered methods sections follow the level of detail required by journals such as Nature Methods and Bioinformatics — sufficient for independent replication.

Methods Catalog

Tools by analysis domain

Quality Control & Preprocessing

5 tools›

FastQCPer-base sequence quality, adapter content, k-mer overrepresentation

MultiQCAggregate QC reports across samples; Nextflow/nf-core integration

fastpAdapter trimming, quality filtering, and per-read QC (preferred over Trimmomatic for speed)

TrimmomaticSliding-window trimming; used for legacy or specific adapter configurations

NanoPlotLong-read QC for Oxford Nanopore data (read length, quality distributions)

Read Alignment & Mapping

6 tools›

STARSplice-aware alignment for RNA-seq; supports two-pass mapping and fusion detection

HISAT2Memory-efficient RNA-seq aligner; graph-based alignment using known splice sites

BWA-MEM2Short-read alignment for DNA-seq (WGS, WES, ChIP-seq); 2× faster than BWA-MEM

minimap2Long-read alignment (PacBio CLR/HiFi, ONT); splice-aware mode for long-read RNA-seq

Bowtie2Short-read alignment for ChIP-seq and small RNA workflows

samtoolsSAM/BAM manipulation, sorting, indexing, flagstat, and depth calculation

Variant Analysis

7 tools›

GATK4 / HaplotypeCallerGermline SNP and indel calling; cohort joint genotyping with GenomicsDBImport

Mutect2Somatic variant calling for tumour–normal pairs and tumour-only modes

DeepVariantDeep learning–based germline caller; consistently top-ranked in benchmarks (GIAB)

Strelka2Somatic small variant and indel calling; computational efficiency for large cohorts

bcftoolsVCF/BCF manipulation, filtering, merging, and stats

VEPVariant Effect Predictor (Ensembl); consequence annotation and CADD/SIFT/PolyPhen integration

SnpEff / ANNOVARFunctional annotation for non-Ensembl reference genomes (crop/livestock species)

RNA-seq Quantification & Differential Expression

7 tools›

STAR + RSEMTranscript-level quantification with alignment-based estimates

SalmonAlignment-free transcript quantification; ultrafast, GC-bias correction

featureCountsGene-level count matrices from BAM files (Subread package)

DESeq2Negative binomial model for differential expression; recommended for most bulk RNA-seq designs

edgeREmpirical Bayes dispersion estimation; preferred for very small sample sizes (n < 3 per group)

limma/voomLinear modelling for complex experimental designs; ANOVA-type contrasts

fgseaFast gene set enrichment analysis (GSEA) and MSigDB pathway analysis

Single-cell & Spatial Transcriptomics

6 tools›

Cell Ranger / STARsoloBarcode demultiplexing and UMI counting for 10x Genomics Chromium and similar platforms

scanpyPython-based single-cell analysis (clustering, trajectory, velocity); AnnData format

Seurat (R)R-based scRNA-seq analysis; reference-based label transfer with Azimuth

scVI / scANVIDeep generative models for batch correction and semi-supervised cell annotation

Monocle3 / PAGAPseudotime and trajectory inference for developmental analyses

Squidpy / MERFISH toolsSpatial transcriptomics analysis; neighbourhood enrichment and spatial statistics

Structural Biology & Molecular Modelling

5 tools›

AlphaFold2 / ColabFoldProtein structure prediction from sequence; multimer complex prediction

ESMFoldLanguage model–based structure prediction; faster for large-scale screening

AutoDock Vina / GninaMolecular docking for drug candidate screening; CNN scoring with Gnina

GROMACSMolecular dynamics simulation; free energy perturbation for binding affinity

PyMOL / ChimeraXStructure visualisation and figure preparation for publications

AI & Machine Learning

6 tools›

PyTorch / LightningPrimary deep learning framework; multi-GPU training and experiment logging

scikit-learnClassical ML (random forests, SVM, logistic regression) for biomarker discovery

XGBoost / LightGBMGradient-boosted trees for tabular genomic and clinical data

HuggingFace TransformersPre-trained genomic language models (DNABERT, Nucleotide Transformer, ESM-2)

SHAPShapley value–based feature importance for model interpretability

MLflowExperiment tracking, hyperparameter logging, and model versioning

Metagenomics & Microbiome

5 tools›

Kraken2 / BrackenTaxonomic classification and abundance estimation from short reads

MetaPhlAn4Strain-level profiling using clade-specific markers

HUMAnN3Functional pathway abundance from shotgun metagenomics

MEGAHIT / MetaSPAdesDe novo metagenomic assembly

QIIME2Amplicon (16S/ITS) diversity analysis; DADA2 denoising integration

This list reflects tools in active use. It is not exhaustive — project-specific tools are documented in the methods section of each deliverable.

Publications

Published work

No records

Publications will appear here

Peer-reviewed articles, preprints, and datasets produced in or with project engagements will be listed here as they are submitted or published. Records include DOI, PMID, and author attribution.

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