Why not a generic FASTQ or CSV converter?

Because the error is almost never “this is not a FASTQ.” It is “this is not a FASTQ this destination will accept.” Each destination gets its own rules and, later, its own landing page.

Will it rename my samples without asking?

No. Identifier changes that could alter scientific meaning are reported and require an explicit choice. Safe, deterministic syntax repairs can be applied automatically.

Which destinations are available today?

None are downloadable yet. Cell Ranger FASTQ names will ship first, as a local program that applies safe renames in the run folder. BCL Convert sample sheets are still planned. Destination landings are published when the job and its delivery are specified, not as empty browsers.

Do you keep the uploaded files?

Run-folder destinations do not upload sequence files. They run on your machine. Future destinations that process file contents on a server will say so first, and those files will be temporary working objects.

Coming soon

Destination-aware bioinformatics file fixer

Generic converters treat FASTQ, sample sheets, and metadata as interchangeable formats. The failure is usually destination-specific: a naming rule, header, identifier, or coordinate convention that one pipeline enforces and another ignores. A browser page cannot rename the files in a sequencing run.

For researchers and core-lab bioinformaticians who have valid data that a named downstream tool will not accept, and who need the repair applied where the files live.

Cell Ranger FASTQ names Get updates

How it works

01
Choose the destination
Select the pipeline or tool that rejected the files—not a generic format pair.
02
Run it where the files are
Download the destination’s program and point it at the folder or sheet that destination requires. The checker uses that tool’s rules, not a universal schema.
03
Review the plan
See structural, naming, metadata, and convention problems before anything is rewritten. Safe repairs are listed separately from inferred ones.
04
Apply unambiguous repairs
Deterministic syntax fixes are applied on disk. Ambiguous changes stay pending until you confirm them. You also get a plain-language change log.

Constraints and checks

Destination profiles added one at a time from real demand
Run-folder destinations shipped as a downloadable for macOS, Windows, and Linux
Validation of structure, naming, headers, identifiers, and coordinate conventions
Deterministic repairs where the transformation is unambiguous
A change report you can keep with the dataset

What it will not do

It is not a universal bioinformatics converter.
It will not rename FASTQs from a browser tab. That job needs a local program.
It will not guess when a transformation could change scientific meaning.
It will not silently rewrite coordinates, strandedness, or sample identity.
Unsupported destinations are not offered as if they were supported.

Destinations, one at a time

Each destination has its own rules and its own page. Run-folder jobs ship as a downloadable. Destinations that are not ready yet are listed as coming soon.

Downloadable · coming soon

Cell Ranger FASTQ filenames

A local program that checks FASTQ names against the Illumina/Cell Ranger convention and applies safe renames in the run folder.

Typical failure: Pipelines reject prefixes with dots, missing lane or read tokens, or files that do not match `_S#_L00#_R#_001.fastq.gz`.

Read the plan →

Coming soon

BCL Convert sample sheet

Validate SampleSheet v1/v2 sections, Sample_ID characters, and index columns against BCL Convert’s actual requirements.

Typical failure: Unrecognized settings, illegal Sample_ID characters, v1/v2 section mismatches, and duplicate IDs abort demultiplexing.

Trust, files, and price

Problems are reported before files are changed
Ambiguous edits are surfaced, not guessed
Every transformation is versioned
Sequence files are not uploaded; run-folder destinations run on your machine
No PHI and no reuse of scientific data for analytics

The Cell Ranger FASTQ renamer is planned as a free downloadable. Other destinations may be priced when they ship.

Get notified when the download is ready

No account is created. We will only use this address to tell you when the program can be downloaded.

Questions

Why not a generic FASTQ or CSV converter?: Because the error is almost never “this is not a FASTQ.” It is “this is not a FASTQ this destination will accept.” Each destination gets its own rules and, later, its own landing page.
Will it rename my samples without asking?: No. Identifier changes that could alter scientific meaning are reported and require an explicit choice. Safe, deterministic syntax repairs can be applied automatically.
Which destinations are available today?: None are downloadable yet. Cell Ranger FASTQ names will ship first, as a local program that applies safe renames in the run folder. BCL Convert sample sheets are still planned. Destination landings are published when the job and its delivery are specified, not as empty browsers.
Do you keep the uploaded files?: Run-folder destinations do not upload sequence files. They run on your machine. Future destinations that process file contents on a server will say so first, and those files will be temporary working objects.