User guide

PlasValidate turns Oxford Nanopore reads of your plasmid into a complete, self-contained validation report for each sample. It assembles the plasmid from scratch with no reference needed, then polishes, annotates and QCs it, and shows the per-base read support behind every call. Everything runs in your browser, with nothing to install.

1 Get started

Create an account on the register page, then sign in. Your uploads and results stay private to your account.

No data handy? Open New run and click Generate example run. It builds a run from a real Oxford Nanopore plasmid sample, so you can walk through the whole thing without uploading anything of your own.

2 The workflow

  1. Upload. On New run, choose your fastq_pass folder. Each barcodeNN sub-folder becomes one sample, and a flat folder of FASTQs is treated as a single barcode. A sample sheet is optional (columns: barcode, alias, approx_size, client, config) and simply names and routes your samples.
  2. Configure. You then land on the configure screen. Give each sample an expected size (leave it blank to let the engine predict it) and a configuration, or use Apply to all to set them in one go. Note that leaving this screen discards the upload.
  3. Submit. Click Submit to queue. Every sample is queued and processing begins, and you can follow progress live on the run page and the console.
  4. Report. When a sample finishes, open its Report, or download the FASTA, GenBank or full export.

3 Reading the report

  • QC verdict. PASS, WARN or FAIL, with every check shown as its value against the threshold, so you can see exactly why the verdict landed where it did.
  • Plasmid map and features. The circular map alongside the annotation table from pLannotate.
  • Base-support viewer. A Sanger-style, per-base view of how the reads support the consensus, with zoom and a marker that tracks onto the map.
  • Multiple sizes and tandems. If the reads suggest several plasmid sizes, each is assembled and the strongest is shown, with the alternatives listed. If a result is a tandem repeat (a concatemer), the monomer is recovered automatically and shown as the primary result.
  • Un-polished draft (WARN). If the final Medaka polishing step fails, PlasValidate still delivers the read-anchored consensus draft, flagged with an amber Un-polished draft banner and a WARN verdict. That draft can carry residual basecalling errors, so treat it as provisional and re-run once the issue is resolved.

4 Storage and retention

  • Raw reads are kept for 24 hours after a run finishes (compressed once it completes), so you can re-run a sample in place, either by requeuing it or by changing its size or configuration and confirming the re-run, without uploading again. After 24 hours the raw reads are removed, so a later re-run means uploading once more.
  • Results are kept for 7 days, after which the run and its deliverables are removed automatically. Download anything you want to keep before then.
  • Each run has an upload limit, and uploads pause automatically if the server is running low on space.

5 Configurations

A configuration bundles the pipeline and QC settings you want to reuse. Everyone gets the built-in Default (read-only); create your own under Configs to tune assembly (including the fallback assembler used when Flye cannot recover a plasmid, and methylation-aware polishing), the QC thresholds, or which report sections to include, then assign it to samples on the configure screen.

? Need help?

Questions, feedback, or a plasmid that did not validate as you expected? Get in touch at contact@plasvalidate.com, or use the contact page.