Step 01
What would you like to analyse?
Select the analysis type matching your experiment. Each pipeline is fully reproducible and delivers publication-ready outputs.
RNA-Seq
Differential expression, pathway enrichment, splice variants, PCA & heatmaps
FASTQ · BAM
Metagenomics
Taxonomic classification, alpha/beta diversity, KEGG functional profiling
FASTQ
Methylation
WGBS / RRBS differential methylation, DMR calling, CpG island analysis
FASTQ · BED
Variant calling
SNP/INDEL detection, structural variants, copy number alterations, annotation
FASTQ · VCF
QC & summary stats
FastQC, MultiQC aggregation, sequencing depth, adapter content, read quality
FASTQ · BAM
Native modifications
Oxford Nanopore base mods — m6A, 5mC, 5hmC — using Dorado basecalling
POD5 · FAST5
Step 02
Upload your sequencing data
Files are staged locally for this dry run. In production, uploads go directly to encrypted cloud storage.
Local dry-run mode
You're running against
localhost:8000. Start the local backend to process real files, or use the simulated flow to test the UI end-to-end.
# Start local backend (Python)
pip install biolome-local
biolome serve --port 8000
# Then re-open this page and upload real files
pip install biolome-local
biolome serve --port 8000
# Then re-open this page and upload real files
📄
—
✓ Staged
Drop files here or click to browse
Select your FASTQ, BAM, CRAM files — max 50 GB
.fastq.gz
.bam
.cram
.vcf
.pod5
.fast5
Step 03
Configure your pipeline
Defaults are pre-filled for most common setups. Adjust for your organism, platform, and desired outputs.
Optional outputs
Publication-ready figures
Volcano plots, heatmaps, PCA — SVG/PDF export
Pathway enrichment (GO / KEGG)
Over-representation analysis on significant hits
MultiQC aggregated report
Interactive HTML QC report across all samples
Reproducible pipeline code
Snakemake workflow — re-run locally at any time
Raw aligned BAM files
Sorted, indexed BAM + BAI — large files, separate download
Step 04
Review & launch
Confirm your pipeline settings. Results will appear on this page and be emailed to you when complete.
Analysis typeRNA-Seq
Input filesample_R1.fastq.gz
Reference genomeGRCh38
PlatformIllumina
Optional outputsFigures · Pathways · MultiQC
Est. turnaround6–14 hours (local: immediate dry run)
Total
$79
🖥
Running in local dry-run mode — no payment required. The pipeline will simulate execution against your local backend at
localhost:8000. Results will be mock data to verify the full flow.Running
Analysis in progress
Your pipeline is executing. Live status below — you can safely close this tab and check your email for results.
Data intake & validation
Validating file format & checksums…
Quality control (FastQC)
Queued
Alignment to reference genome
Queued
Quantification & differential expression
Queued
Pathway enrichment (GO / KEGG)
Queued
Figure generation & report assembly
Queued
✓ Analysis complete — dry run
Results ready
All outputs are available below and have been sent to your delivery email. This is mock data from the dry run.
Total reads
48.2M
✓ High depth
Mapping rate
94.7%
✓ Excellent
Sig. DEGs
1,847
734 up · 1,113 ↓
Q30 score
91.3%
✓ Pass
📁
In local mode, output files would be written to
./biolome_results/ on your machine. In cloud mode, signed download links are emailed to you.
MultiQC report
multiqc_report.html · 4.2 MB
HTMLDEG results table
deg_results_full.csv · 1.8 MB
CSVPublication figures
figures_package.zip · 18.4 MB
SVG / PDFPathway enrichment
go_kegg_results.xlsx · 340 KB
XLSXAnalysis summary PDF
biolome_report.pdf · 2.1 MB
PDFSnakemake pipeline
pipeline.smk · 14 KB
SNAKEMAKE