Why not a generic FASTQ or CSV converter?

The error is almost never “this is not a FASTQ.” It is “this is not a FASTQ this pipeline will accept.” Each destination gets its own rules and its own page.

Will it rename my samples without asking?

No. Identifier changes that could alter scientific meaning are reported and need a choice. Safe syntax repairs can be applied automatically.

Which destinations are available today?

None to download yet. Cell Ranger FASTQ names ship first, as a local program. BCL Convert sample sheets are still planned.

Do you keep the uploaded files?

Run-folder jobs do not upload sequence files. They run on your machine. If a later destination processes files on a server, that page will say so first.

Coming soon

File repairs for a named pipeline

Generic converters treat FASTQ, sample sheets, and metadata as interchangeable. The failure is usually 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 people with valid data that a named tool will not accept, who need the repair applied where the files live.

Cell Ranger FASTQ names Get updates

How it works

01
Choose the pipeline
Pick the tool that rejected the files, not a generic format pair.
02
Run it where the files are
Download that destination’s program and point it at the folder or sheet. It uses that tool’s rules.
03
Review the plan
See naming, header, and convention problems before anything is rewritten. Safe repairs are listed separately from inferred ones.
04
Apply unambiguous repairs
Clear syntax fixes go on disk. Ambiguous changes stay pending until you confirm them. You also get a change log.

Constraints and checks

One pipeline at a time, added from real demand
Run-folder jobs as a download for macOS, Windows, and Linux
Checks for structure, naming, headers, identifiers, and coordinate conventions
Deterministic repairs when the transformation is unambiguous
A change report you can keep with the dataset

What it will not do

Not a universal bioinformatics converter.
Will not rename FASTQs from a browser tab.
Will not guess when a change could alter scientific meaning.
Will not silently rewrite coordinates, strandedness, or sample identity.
Unsupported pipelines are not offered as if they were supported.

What’s planned

Each pipeline has its own rules and its own page. Run-folder jobs ship as a download. 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`.

See the page →

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.

Price and your files

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

Paid when it ships. The price will be on this page. Browser tools stay free.

Email when the download is ready

We’ll write when you can buy and download it. That’s it.

Questions

Why not a generic FASTQ or CSV converter?: The error is almost never “this is not a FASTQ.” It is “this is not a FASTQ this pipeline will accept.” Each destination gets its own rules and its own page.
Will it rename my samples without asking?: No. Identifier changes that could alter scientific meaning are reported and need a choice. Safe syntax repairs can be applied automatically.
Which destinations are available today?: None to download yet. Cell Ranger FASTQ names ship first, as a local program. BCL Convert sample sheets are still planned.
Do you keep the uploaded files?: Run-folder jobs do not upload sequence files. They run on your machine. If a later destination processes files on a server, that page will say so first.