Configure with practical inputs
Provide files, references, parameters, and other required inputs through a structured pipeline form.
Managed bioinformatics pipelines
Managed Bioinformatics Pipelines for Genomic Research
GenomeMiner gives research teams a structured way to configure, run, follow, and retain genomic analyses. Inputs, parameters, execution details, logs, and outputs remain connected to the workspace where the research is conducted.
Pipeline coverage
Support across every stage of genomic analysis
Select the analyses that fit the research question while keeping each run connected to its data, configuration, and results.
- Stage 01
Prepare sequencing data
Process Illumina and Nanopore reads, perform basecalling or alignment, and review sequencing quality before downstream analysis.
Typical route: raw reads and references → processed reads, alignments, and quality reports
Illumina Read Processing · Nanopore Read Processing · Dorado · Minimap2 · NanoPlot
- Stage 02
Build and evaluate genomes
Run long-read, short-read, or hybrid assembly pipelines and assess the resulting genome or assembly quality.
Typical route: sequencing reads → assembled genome files and assessment reports
Canu · Flye · Hifiasm · Unicycler · BUSCO · Merqury
- Stage 03
Characterize microbial biology
Annotate genomes, examine taxonomy, identify biosynthetic gene clusters, and investigate antimicrobial resistance or mobile elements.
Typical route: assembled genomes or reads → annotation, taxonomy, BGC, AMR, and mobile-element results
Prokka · MiGA Taxonomy · MetaPhlAn 4 · BGC Identification · AMRFinderPlus · PlasmidFinder · geNomad
- Stage 04
Compare and extend the analysis
Continue with variant analysis, genome comparison, functional analysis, transcriptomics, methylation analysis, or selected machine-learning pipelines.
Typical route: genomes, VCFs, or expression data → comparison, variant, and functional results
Nanopore Variant Calling · VCF Sample Diff · Plotsr · GSEApyEnricher
Managed execution
The analysis stays connected to the research program
Follow each run
Review active and historical analyses, status, execution details, and logs without reconstructing the process.
Retain outputs with context
Inspect or download results and retain output data in the workspace for continued research.
Work across the team
Give researchers, computational specialists, and external partners appropriate visibility into the same program.
Explore more of GenomeMiner
Microbial genome analysisFollow reads through assembly, assessment, annotation, and microbial characterization.Custom bioinformatics pipelinesTurn an existing specialist analysis into a managed, repeatable service.Genomic data managementKeep research files, analysis history, and outputs connected in one workspace.
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.