Organize each candidate
Keep sample information, sequencing files, assemblies, and analysis outputs in a shared research workspace.
Microbial genome analysis
Microbial Genome Analysis from Sequencing Reads to Biological Insight
GenomeMiner connects the practical stages of microbial genome analysis so discovery teams can compare candidates without separating sequencing files, pipeline runs, quality evidence, and biological results.
Representative pipeline
Move from reads to a traceable evidence package
Build the route that matches each dataset and research objective. Every stage retains the context needed to review the candidate and continue the analysis.
- Stage 01
Review and prepare reads
Bring Illumina or Nanopore data into the workspace and review processing or quality outputs before assembly.
Input: sequencing reads → Output: processed reads and QC evidence
FASTQ inputs · read processing · NanoPlot
- Stage 02
Assemble the genome
Choose a long-read, short-read, or hybrid assembly route appropriate to the available sequencing data.
Input: prepared reads → Output: assembled genome files
Flye · Canu · Hifiasm · Unicycler
- Stage 03
Assess assembly quality
Retain assembly assessment alongside the input reads, assembly run, and resulting genome files.
Input: assembled genomes and supporting reads → Output: assessment reports
BUSCO · Merqury · assembly outputs
- Stage 04
Characterize the organism
Continue through taxonomy, annotation, biosynthetic gene clusters, antimicrobial resistance, plasmids, and mobile elements.
Input: assembled genomes or reads → Output: biological characterization results
MiGA Taxonomy · Prokka · BGC Identification · AMRFinderPlus · PlasmidFinder · geNomad
For microbial discovery teams
Compare candidates without losing the evidence behind them
Review quality consistently
Follow the same analysis route across candidates while retaining the status and outputs of each run.
Connect biological results
Keep taxonomy, annotation, BGC, AMR, and mobile-element results associated with the candidate that produced them.
Share a reviewable history
Give collaborators access to the relevant data, analysis history, and outputs when candidates are reviewed.
Free project pilot
Run your own data through GenomeMiner, free.
Tell us about your project. We'll set up a workspace, recommend the right pipelines, and provide free credits so you can evaluate GenomeMiner on real research, not a demo dataset.
Request a free pilotPilot access and credits are scoped to your project.
- Free pilot with pipeline credits
- No infrastructure to set up
- Bring your existing pipelines
How the pilot works
- 1Tell us about your data and research goal.
- 2We identify the right pipelines and allocate credits for your project.
- 3Your team runs real analyses in its own GenomeMiner workspace.