Rootline Genomics PLANT GENOMICS · BIOINFORMATICS

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 & annotation

Take raw reads all the way to a reference you can build on. I assemble or rescue a draft, polish to high base accuracy, resolve and mask the repeat landscape, and add evidence-based structural gene models — one continuous workflow that ends in a genome ready to annotate functionally and compare.

Deliverables

  • QC report: contiguity, BUSCO, QV
  • Polished / curated assembly
  • Repeat library & masked assembly
  • GFF3 gene models + transcript/protein FASTA
  • Browser-ready tracks

Example projects

  • De novo assembly + annotation of a new genome
  • Rescue & re-annotation of a fragmented draft
  • Haplotype-aware assembly and curation

You provide

  • Raw reads or an existing assembly
  • Platform & coverage details
  • Any RNA-seq and related-species proteins

S02

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, transcription factors, 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

S03

Comparative genomics

Put your genome in context. I compare genomes to find orthologs, synteny, gene-family expansions and contractions, and lineage-specific features — the basis for evolutionary and functional insight, including pan-genomes of related isolates.

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

S04

Population genomics

Understand variation within and between populations. From genotyping to interpretation: I call and filter variants, quantify diversity and population structure, reconstruct demographic history, and scan for signatures of selection — from short-read, GBS, or whole-genome data.

Deliverables

  • Filtered variant set (VCF)
  • Diversity & differentiation (π, FST, Tajima’s D)
  • Structure: PCA / admixture
  • Selection scans + figures

Example projects

  • Landscape genomics of a crop wild relative
  • Structure across accessions or isolates
  • Selection scan in a pathogen population

You provide

  • Reads or an existing VCF
  • Reference genome
  • Sample & population metadata

S05

GWAS & QTL mapping

Find the loci behind a trait. I run genome-wide association (GWAS) and linkage-based QTL mapping with careful population-structure control and phenotype QC, then follow up with candidate genes under the peaks and heritability estimates.

Deliverables

  • Association / QTL results
  • Manhattan & QTL plots, thresholds
  • Candidate genes under peaks
  • Heritability estimates + methods

Example projects

  • GWAS for disease resistance in a panel
  • QTL mapping in a bi-parental population
  • Meta-analysis across trials or years

You provide

  • Genotypes (VCF / array / GBS)
  • Phenotype data & experimental design
  • Reference & annotation, if available

S06

RNA-seq, transcriptomics & co-expression

Find out what’s expressed, when, and with what. I run differential expression, time courses, and dual host–pathogen RNA-seq, and build co-expression networks (e.g. WGCNA) to find modules and hub genes — all translated into clear biology.

Deliverables

  • QC & alignment
  • Normalized counts & DE tables
  • Enrichment analysis
  • Co-expression modules & hub genes
  • Volcano / heatmap / network figures

Example projects

  • Host response across infection timepoints
  • Co-expression modules for a trait
  • Treatment vs control with replicates

You provide

  • Raw reads + sample metadata
  • Reference or assembly

S07

Spatial transcriptomics

See where genes are expressed in the tissue. I process spatial transcriptomics data (Visium and related platforms): QC, clustering, spatially variable genes, deconvolution, and integration with single-cell or bulk references — connecting expression to anatomy.

Deliverables

  • Spot / cell QC
  • Spatial clusters & annotation
  • Spatially variable genes
  • Deconvolution / integration
  • Spatial expression figures

Example projects

  • Expression across a root or leaf cross-section
  • Mapping gene activity at an infection site
  • Domain-level marker discovery

You provide

  • Spatial data + tissue images
  • Reference / annotation
  • Experimental design

S08

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

S09

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

S10

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)

S11

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.

Start a project