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 workflow
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
Try GenomeMiner with your own research project.
Discuss your project with us and we'll provide free platform access and pipeline credits matched to your data and analysis needs.
1Tell us about your data and research goal.
2We'll identify relevant pipelines and an appropriate credit allocation.
3You'll receive free platform access to evaluate GenomeMiner with your project.