LabscoMCP early access ↗
coreymhudsonMCP SERVER

MCP Sequence Simulation Server

Generate DNA and protein sequences, mutate them, evolve populations, and simulate NGS reads with platform-specific error models.

by coreymhudson ↗Biomedical: Genomics & Clinical DataCommunity

LABSCO SUMMARY

Test data for a pipeline, with the ground truth known.

Benchmarking a variant caller or an assembler needs reads whose true answer you already hold. This generates the sequence, applies the evolutionary model, and simulates the reads on top — so the expected result exists before the pipeline runs.

What it is

A simulation server for molecular sequence data. DNA and protein sequences are generated under models you choose, then mutated, evolved across populations, or dropped down a phylogenetic tree — and sequencing reads can be simulated on top of any of it.

What you get

  • DNA generated at a specified GC content, from a Markov chain model, or with codon bias for realistic coding sequences
  • Protein sequences generated uniformly, hydrophobic-biased, disorder-prone, or from an amino acid composition you supply
  • NGS reads simulated with Illumina, 454, Ion Torrent or PacBio quality models, single-end or paired-end, to a coverage depth you set
  • Substitutions with transition/transversion bias plus insertions and deletions, tracked over multiple iterations
  • Population evolution over generations with configurable fitness functions and lineage tracking
  • Sequences evolved on a phylogenetic tree under JC69, K80, HKY85 or GTR, with a uniform or variable molecular clock, written as FASTA, NEXUS or PHYLIP

Requirements

Node with npm install and npm run build, then one stdio entry pointing at the built server. No account and no key — everything is generated locally, and a seed makes a run reproducible.

Setup effort

Build from source — git clone https://github.com/coreymhudson/mcp-sequence-simulation.git

See installation options