Services
What I can do for your lab.
Consulting across the genomics and bioinformatics workflow, from raw reads to manuscript. Engagements range from a focused analysis or assembly review to an end-to-end genome resource. Every project ends with interpreted results, documented methods, and figures you can use.
S01
Genome assembly & polishing review
Assess and improve a draft, or assemble from raw reads. I evaluate contiguity, completeness, and base accuracy, find what's limiting quality, and polish or re-scaffold to a reference you can confidently annotate and compare.
Deliverables
- QC report: contiguity, BUSCO, QV
- Polished / curated assembly
- Contaminant & organelle screen
- Recommendations memo
Example projects
- De novo assembly from Nanopore + Illumina
- Rescue of a fragmented draft
- Haplotype-aware assembly review
You provide
- Raw reads or existing assembly
- Platform & coverage details
- Genome size / ploidy, if known
S02
Genome annotation (structural)
Predict where the genes are. I build evidence-based structural annotations using RNA-seq and protein evidence, producing gene models you can trust for everything downstream.
Deliverables
- GFF3 gene models
- Transcript & protein FASTA
- Annotation QC (protein BUSCO, stats)
- Browser-ready tracks
Example projects
- First annotation of a new genome
- Re-annotation with added RNA-seq
- Lifting annotations across assemblies
You provide
- Assembly
- Any RNA-seq reads
- Related-species proteins, if available
S03
Functional annotation
Say what the genes do. I assign putative functions, domains, pathways, and gene families, with attention to the categories that matter for your biology, such as effectors, CAZymes, or resistance genes.
Deliverables
- Functional tables: GO, KEGG, Pfam/InterPro
- Curated gene sets of interest
- Enriched-function summary
Example projects
- Effector & CAZyme catalog for a pathogen
- NLR / R-gene survey in a host
- Secondary-metabolite gene clusters
You provide
- Gene models or proteins
- The functional categories you care about
S04
Repeat annotation
Map the repetitive landscape. I identify and classify transposable elements and repeats. This matters for clean gene annotation and for understanding genome size and evolution.
Deliverables
- De novo repeat library
- Masked assembly
- TE classification & landscape
- Repeat-content report
Example projects
- TE annotation for a new genome
- Repeat content across isolates
- Resolving repeat-driven assembly issues
You provide
- Assembly
- Any existing repeat libraries
S05
Comparative genomics
Put your genome in context. I compare genomes to find orthologs, synteny, gene-family expansions and contractions, and lineage-specific features. This is the basis for evolutionary and functional insight.
Deliverables
- Orthology & synteny analyses
- Gene-family dynamics
- Phylogenomic trees
- Figures: dotplots, trees, UpSet
Example projects
- Pan-genome of related isolates
- Synteny across a clade
- Expansion of a virulence-associated family
You provide
- Genomes / annotations to compare
- The comparative question
S06
RNA-seq & transcriptomics
Find out what's expressed, and when. I run differential expression and co-expression analyses, including dual host-pathogen RNA-seq and time courses, and translate them into clear biological findings.
Deliverables
- QC & alignment
- Normalized counts & DE tables
- Enrichment analysis
- Volcano / MA / heatmap figures
Example projects
- Host response across infection timepoints
- Pathogen programs by tissue
- Treatment vs control with replicates
You provide
- Raw reads + sample metadata
- Reference or assembly
S07
DNA methylation & modified bases
Read the epigenome. I analyze cytosine methylation from bisulfite / EM-seq and modified-base signal from Nanopore, with context-aware (CpG / CHG / CHH) profiling and differential methylation.
Deliverables
- Per-context methylation calls
- DMR tables
- Metaplots & genome-wide profiles
- Cross-platform comparison + methods
Example projects
- Methylome across developmental stages
- DMRs during infection
- Bisulfite vs Nanopore concordance
You provide
- Reads: bisulfite / EM-seq or Nanopore
- Reference / assembly
- Experimental design
S08
Metabarcoding & barcode benchmarking
Know what's in the sample. I build amplicon pipelines (ASV / OTU), assign taxonomy, and benchmark markers, primers, and reference databases so your survey design is defensible.
Deliverables
- ASV / OTU tables
- Taxonomic assignment
- Diversity & composition figures
- Marker / primer benchmarking report
Example projects
- Plant DNA metabarcoding of mixed samples
- Primer comparison for a target group
- Rhizosphere community profiling
You provide
- Amplicon reads
- Marker / primer info
- Sample metadata
S09
Custom bioinformatics pipelines
Make it reproducible and repeatable. I build documented, parameterized pipelines for your recurring analyses, so your lab can re-run them long after the project ends.
Deliverables
- Versioned, documented pipeline
- Environment / config files
- Usage documentation
- Handoff session
Example projects
- Standardized assembly to annotation workflow
- Lab-wide RNA-seq pipeline
- Reusable methylation pipeline
You provide
- Representative data
- Target compute environment (HPC / cloud / local)
S10
Manuscript-ready figures & methods
Get the manuscript over the line. I produce clean, consistent figures and write the methods and analysis sections, so your results are reproducible and review-ready.
Deliverables
- Vector / high-res figures
- Figure legends
- Methods & supplementary text
- Reproducible figure code
Example projects
- Genome resource / announcement package
- Figure overhaul for revision
- Methods for a multi-omics paper
You provide
- Final results / data
- Target journal style
- Deadlines
Not sure which of these you need?
Most projects combine a few. Describe your data and your goal, and I'll propose a scope.