How is this different from the batch processor?

The Batch Processor runs one tool over every record. The Batch Workflow chains several tools into a pipeline: each step's sequence output becomes the next step's input, so you can run multi-stage analyses — e.g. reverse complement → translate → protein properties — over the whole file at once.

Where does each step's input come from?

By default a step reads the sequence produced by the previous step. A step can also draw from the initial record or from any earlier step that emits a sequence, so you can build branched or re-based pipelines. Steps that don't emit a sequence (for example a properties report) can only be the final step.

Can I run the same pipeline from code?

Yes. The pipeline is executed by POST /api/v1/workflow with a list of steps and your input, and every underlying tool is also available individually over the REST API and the MCP server.

How many records and steps are supported?

Runs are synchronous and capped for responsiveness — up to a few hundred records and several pipeline steps per run. For larger jobs, split the input or call the API in batches.

Batch Workflow — Multi-Tool Sequence Pipelines Over a FASTA

Chain several tools into a pipeline and run it over every record in a multi-FASTA.

🌐 Runs on the SeqBench API — also callable via REST & MCP, and in bulk from the batch tools

Go beyond a single operation: assemble a pipeline of SeqBench tools and run it across a whole multi-FASTA in one pass. Each step takes the sequence produced by the previous step (or the original record, or any earlier step), so you can reverse-complement, translate, then analyse the resulting protein — or design any chain that fits your workflow. Every step runs on the SeqBench API, and the same pipeline is callable programmatically via POST /api/v1/workflow. Inspect the per-record step-by-step trace and download the combined results as CSV or TSV.

Multi-FASTA input (or one sequence per line)

0 records detected

Pipeline steps

Chain several tools into a pipeline — e.g. reverse-complement → translate → protein properties — and run it over every record at once. Each step feeds its sequence into the next. The same pipeline runs programmatically via POST /api/v1/workflow.

How to use the Batch Workflow tool

1Paste a multi-FASTA file, or one sequence per line.
2Add pipeline steps and pick a tool for each; by default each step's sequence output feeds the next (you can also draw from the initial record or an earlier step).
3Run the pipeline over every record, expand any record to see its per-step trace, and download the combined CSV/TSV table.

Frequently asked questions

How is this different from the batch processor?: The Batch Processor runs one tool over every record. The Batch Workflow chains several tools into a pipeline: each step's sequence output becomes the next step's input, so you can run multi-stage analyses — e.g. reverse complement → translate → protein properties — over the whole file at once.
Where does each step's input come from?: By default a step reads the sequence produced by the previous step. A step can also draw from the initial record or from any earlier step that emits a sequence, so you can build branched or re-based pipelines. Steps that don't emit a sequence (for example a properties report) can only be the final step.
Can I run the same pipeline from code?: Yes. The pipeline is executed by POST /api/v1/workflow with a list of steps and your input, and every underlying tool is also available individually over the REST API and the MCP server.
How many records and steps are supported?: Runs are synchronous and capped for responsiveness — up to a few hundred records and several pipeline steps per run. For larger jobs, split the input or call the API in batches.

Related tools

Sequence Analyzer

Generate composition, ORF, restriction-site and primer summaries from one sequence.

Cloning Simulator

Assemble fragments and design junction primers for Gibson, Golden Gate or restriction cloning.

Batch Processor

Apply one operation to every record in a multi-FASTA and export a single CSV/TSV table.