Standard Analysis Pipelines: Submit Online, Run After Review

How it works

Submitted in the client portal, run after review

Sign in and submit

In your project in the client portal, choose a pipeline, use data already uploaded to the project or public accession numbers as input, set the parameters and submit.

Expert review

Our bioinformaticians review the data and parameters, and the run starts once they approve it. We tell you the cost during the review.

Run completes

The result files are added to your project deliverables and we email you.

Preview, then pay

You preview the results online first; every file unlocks once payment is received.

The pipelines

10 standard pipelines

Projects treated as human data can only run pipelines on public accession numbers (e.g. SRR / GSE), not on uploaded raw data.
Small, non-human projects can submit these pipelines in the client portal after signing in. For larger projects, contact us; teams in mainland China can also use Research Compute.
For analysis built around your research question, see custom analysis.

RNA-seq pipeline: FASTQ to QC, alignment, quantification, expression matrix and QC report.
Single-cell RNA-seq pipeline: FASTQ to cell × gene matrices and QC report.
16S / ITS amplicon pipeline: ASV inference, taxonomy, diversity analysis and report.
Metagenomic taxonomic profiling pipeline: Taxonomic profiles from several classifiers with a summary report.
Variant calling pipeline (non-human): Alignment, duplicate marking, variant calling and annotation.
ChIP-seq pipeline: Alignment, peak calling, QC and bigWig tracks.
ATAC-seq pipeline: Alignment, accessible-region peak calling and QC.
Methylation sequencing pipeline: Bisulfite alignment and methylation calling.
Differential abundance pipeline: Differential analysis, enrichment and interactive report from a count matrix.
Public data retrieval: Download raw data and metadata by GEO / SRA / ENA accession.

Submit a pipeline in the client portal

Not sure which pipeline fits, or need a full analysis? Ask us first.

Standard pipelines (run after review)