Services
Every analysis your science needs.
Eight automated pipelines, bespoke custom analytics, and expert consultation — all built for reproducibility, speed, and publication-ready output.
8
Automated Pipelines
4–24h
Turnaround
Free
First Consultation
∞
Organisms
RNA-Seq Analysis · running · 1h 22m elapsed
Metagenomics · completed · 14s ago
Methylation Profiling · queued
Variant Detection · completed · 3m ago
Native Modifications · running · 47m elapsed
Summary Statistics · completed · 8m ago
Haplotype & Allele · queued
Data Preprocessing · running · 12m elapsed
RNA-Seq Analysis · running · 1h 22m elapsed
Metagenomics · completed · 14s ago
Methylation Profiling · queued
Variant Detection · completed · 3m ago
Native Modifications · running · 47m elapsed
Summary Statistics · completed · 8m ago
Haplotype & Allele · queued
Data Preprocessing · running · 12m elapsed
Automated pipelines
Click-button genomics — no command line required.
Upload your raw data, choose your pipeline, configure outputs. Results delivered to your inbox in hours.
01
RNA-Seq Analysis
Differential expression, pathway enrichment, publication-ready figures
from$39
+
$ biolome run rna-seq --samples 6 # Aligning reads — STAR v2.7.10a | hg38 mean mapping rate: 94.2% # Differential expression — DESeq2 significant DEGs: 847 (padj < 0.05) upregulated: 423 | downregulated: 424 # Outputs DEG_table.csv volcano.pdf heatmap.pdf
What's included
Full bulk RNA-Seq workflow from raw reads to publication-ready figures. Supports single and multi-group comparisons.
- DESeq2 & edgeR differential expression
- Pathway enrichment (KEGG, GO, Reactome)
- Volcano plots, heatmaps, PCA
- Gene-level and transcript-level quantification
- Pseudo-bulk single-cell support
Launch pipeline →
from $39 / run
02
Metagenomics
Taxonomic profiling, alpha/beta diversity, functional annotation
from$49
+
$ biolome run metagenomics --type shotgun # Taxonomic classification — Kraken2 + Bracken samples processed: 12 species detected: 341 (conf ≥ 0.05) # Diversity analysis alpha metrics: Shannon, Simpson, Chao1 beta metrics: Bray-Curtis, UniFrac # Outputs taxonomy.html diversity.pdf otu_table.biom
What's included
End-to-end metagenomic analysis from amplicon or shotgun sequencing. Supports short and long reads.
- Taxonomic profiling (kingdom to species)
- Alpha & beta diversity analysis
- Functional annotation (HUMAnN3)
- Differential abundance testing
- Nanopore long-read support
Launch pipeline →
from $49 / run
03
Methylation Profiling
Genome-wide CpG methylation, DMR calling, differential methylation
from$59
+
$ biolome run methylation --type WGBS # Alignment — Bismark | hg38 | 96.1% mapped CpG sites profiled: 24.8M # Differential methylation — DSS DMRs identified: 1,847 (q < 0.05) mean delta-beta: 0.38 # Outputs DMR_report.html methylation.bedgraph lollipop.pdf
What's included
Comprehensive methylation analysis supporting WGBS, RRBS, and Nanopore native bisulfite-free approaches.
- Genome-wide CpG methylation calling
- DMR detection (DSS / metilene)
- Differential methylation analysis
- CpG island and shore annotation
- Nanopore native methylation support
Launch pipeline →
from $59 / run
04
Variant Detection
SNP, INDEL, structural variant, and CNV calling with annotation
from$59
+
$ biolome run variant-detection --platform nanopore # Variant calling — Clair3 + Sniffles2 SNPs: 4.2M | INDELs: 187K structural variants:2,341 | CNVs: 89 # Annotation — ClinVar, gnomAD, dbSNP high-impact SNPs: 2,847 (CADD > 20) # Outputs filtered.vcf.gz sv_report.pdf igv.xml
What's included
Comprehensive variant calling for short and long reads, with clinical and population-level annotation.
- SNP, INDEL, and structural variant calling
- Copy number variation (CNV) analysis
- ClinVar, gnomAD, dbSNP annotation
- Population frequency and impact filtering
- ONT and PacBio long-read support
Launch pipeline →
from $59 / run
05
Native Modifications
Direct detection of m6A, 5mC, 5hmC from Nanopore native sequencing
from$69
+
$ biolome run native-mods --mod m6A,5mC # Basecalling — Dorado v0.6 | sup model reads processed: 8.4M # Modification calling — Modkit m6A sites: 142,847 5mC sites: 31.2M # Motif enrichment: DRACH detected # Outputs modkit.bed mod_summary.html pileup.bigwig
What's included
Single-nucleotide resolution base modification detection from Nanopore native sequencing — no bisulfite conversion needed.
- m6A, 5mC, 5hmC detection (Dorado)
- Single-nucleotide resolution calling
- Motif analysis and DRACH enrichment
- Per-read and aggregate pileup outputs
- PromethION and MinION support
Launch pipeline →
from $69 / run
06
Data Preprocessing & QC
Trimming, alignment, format conversion — BAM, FASTQ, CRAM, VCF, POD5
from$29
+
$ biolome run preprocess --input sample.fastq.gz # QC & trimming — fastp reads passed: 98.7% (of 42.3M total) adapter detected: Illumina TruSeq # Alignment — minimap2 / BWA-MEM2 mapping rate: 98.2% # Outputs trimmed.fastq.gz aligned.bam qc_report.html
What's included
Flexible preprocessing for any sequencing data type — our most used pipeline as an upstream step to other analyses.
- Adapter trimming and quality filtering (fastp)
- Format conversion (BAM, FASTQ, CRAM, VCF)
- Alignment (BWA-MEM2, STAR, minimap2)
- Duplicate marking and coordinate sorting
- Comprehensive fastp HTML QC report
Launch pipeline →
from $29 / run
07
Summary Statistics & QC
FastQC, MultiQC, depth-of-coverage, publication-ready QC reports
from$39
+
$ biolome run qc-stats --input aligned.bam # Per-sample QC — FastQC + MultiQC mean depth: 32.4x genome coverage: 97.1% (at 1x) duplication rate: 4.3% insert size: 186 bp (sd 42) # Outputs multiqc_report.html coverage.pdf stats.tsv
What's included
Comprehensive QC across all samples in a single aggregated report. Ideal before committing to downstream analysis.
- Per-sample FastQC metrics
- Multi-sample MultiQC aggregation
- Depth-of-coverage analysis (mosdepth)
- GC bias, duplication, and insert size
- Publication-ready interactive HTML report
Launch pipeline →
from $39 / run
08
Haplotype & Allele Analysis
Phased haplotype reconstruction, allele frequency estimation, population genotyping
from$59
+
$ biolome run haplotype --phasing statistical # Read phasing — WhatsHap | long reads phased blocks: 1,847 phase block N50: 2.3 Mb # Allele frequency analysis heterozygous sites: 892K | HWE pass: 99.1% # Outputs phased.vcf.gz haplotype_map.pdf allele_freq.tsv
What's included
Phase-resolved haplotype analysis for short and long reads. Supports trio-based phasing and population-level workflows.
- Phased haplotype reconstruction (WhatsHap)
- Allele frequency estimation
- Population-level HWE testing
- ONT and PacBio long-read phasing
- Trio-based phasing available
Launch pipeline →
from $59 / run
How it works
From raw files to results — in four steps.
01
Choose your pipeline
Select from 8 automated analysis types, or request a custom project. Not sure which fits? Book a free consultation first.
02
Upload your data
Drag-and-drop FASTQ, BAM, CRAM, POD5, VCF, or BED files. Secure TLS transfer with 30-day retention.
03
Configure your run
Set reference genome, platform, library type. Toggle optional outputs: pathway enrichment, publication figures, pipeline code.
04
Receive your results
Publication-ready figures, count tables, QC reports, and aligned files delivered by email in 4–24 hours.
Pipeline comparison
Find the right fit for your data.
| Pipeline | Primary input | Diff. expression | Figures | Long-read | Starting price |
|---|---|---|---|---|---|
RNA-Seq | FASTQ / BAM | ✓ | ✓ | — | $39 |
Metagenomics | FASTQ | — | ✓ | ✓ | $49 |
Methylation Profiling | FASTQ / BED | ✓ | ✓ | ✓ | $59 |
Variant Detection | FASTQ / VCF | — | ✓ | ✓ | $59 |
Native Modifications | POD5 / FAST5 | — | ✓ | ✓ | $69 |
Data Preprocessing | BAM / FASTQ / VCF | — | — | ✓ | $29 |
Summary Statistics | FASTQ / BAM | — | ✓ | ✓ | $39 |
Haplotype & Allele | FASTQ / VCF | — | ✓ | ✓ | $59 |