1.2.0

Nextclade Web 1.4.0, Nextclade CLI 1.2.0, Nextalign CLI 1.2.0 (2021-06-24)

Nextclade Web and Nextclade CLI

[New feature] Quality control (QC) rules: "Frame shifts" (F) and "Stop codons" (S)

We have added two additional QC rules designed to flag sequences that likely do not correspond to functional viruses.

"Stop codons" rule (S)

Checks if any of genes have premature stop codons. A stop codon within a gene will now result in a QC warning, unless it is one of the very common stop codons in ORF8 at positions 27 or 68. This list of ignored stop codons is defined in the stopCodons.ignoredStopCodons property of the QC configuration file (qc.json) and can be adjusted. The default list might be extended in the future.

Results of this check are available in JSON, CSV, and TSV output files as qc.stopCodons. In Nextclade Web it is displayed in the "QC" column of the results table as a circle with letter "S" in it.

"Frame shifts" rule (F)

Checks and reports if any of the genes have a length that is not divisible by 3. If at least one such gene length is detected, the check is considered "bad". Failure of this check means that the gene likely fails to translate.

Results of this check are available in JSON, CSV, and TSV output files as qc.frameShifts. In Nextclade Web it is displayed in the "QC" column of the results table as a circle with letter "F" in it.

[Change] Quality control (QC) configuration file updated

New entries were added to the QC configuration file (qc.json) for the two new rules. For Nextclade CLI users, we recommend to download the new file from our data/ directory on GitHub.

This file is now versioned using the new schemaVersion property. If the version of qc.json is less than the version of Nextclade CLI itself, users will now receive a warning.

All QC checks are now optional: a rule that has no corresponding config object is automatically disabled.

[Bug fix] CSV/TSV output files corrected

This release corrects a few issues with CSV/TSV output files:

• quotation marks are now escaped correctly
• special characters are now surrounded with quotes
• line breaks are now encoded as CR LF for better compatibility and consistency with Nextclade 0.x
• column shifts are now prevented in CSV/TSV results when some of the QC checks are disabled, as disabled checks return empty strings as result

Nextclade Web

[Bug fix] Ranges displayed off-by-one in GUI

Ranges displayed in Nextclade Web were off-by-one due to a front-end bug. Ends of ranges (right boundaries) were extending one unit too far. This means that alignment ranges, missing nucleotide ranges, ranges of gaps, not-sequenced ranges, were all displayed 1 unit longer than they should have been be. This release fixes this problem.

Only the display in the results table of Nextclade Web is affected. None of the output files, either produced by Nextclade CLI or by Nextclade Web are affected.

[New feature] Insertions displayed in the results table

A new column for insertions (abbreviated as "Ins.") was added to the results table of Nextclade Web. It shows the total number of inserted nucleotides. Hovering reveals more details about each insertion. This information was already available in the output files, and is now also shown in the GUI.

Nextalign CLI

There are no changes in Nextalign in this release, but we keep versions of Nextalign and Nextclade in sync.