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@nextstrain-bot nextstrain-bot released this 24 Jan 13:07
2.10.0
da1928e

Nextclade Web 2.10.0, Nextclade CLI 2.10.0 (2023-01-24)

Add motifs search

Nextclade datasets can now be configured to search for motifs in the translated sequences, given a regular expression.

At the same time, we released new versions of the following Influenza datasets, which use this feature to detect glycosylation motifs:

  • Influenza A H1N1pdm HA (flu_h1n1pdm_ha), with reference MW626062
  • Influenza A H3N2 HA (flu_h3n2_ha), with reference EPI1857216

If you run the analysis with the latest version of these datasets, you can find the results in the glycosylaiton column or field of output files or in "Glyc." column in Nextclade Web.

If you want to configure your own datasets for motifs search, see an example configuration in the aaMotifs property of virus_properties.json of these datasets: link.

Allow to chose columns written into CSV and TSV outputs

You can now select a subset of columns to be included into CSV and TSV output files of Nextclade Web (available in the "Download" dialog) and Nextclade CLI (available with --output-csv and --output-tsv). You can either chose individual columns or categories of related columns.

In Nextclade Web, in the "Download" dialog, click "Configure columns", then check or uncheck columns or categories you want to keep. Note that this configuration persists across different Nextclade runs.

In Nextclade CLI, use --output-columns-selection flag. This flag accepts a comma-separated list of column names and/or column category names. Individual columns and categories can be mixed together. You can find a list of column names in the full output file. The following categories are currently available: all, general, ref-muts, priv-muts, errs-warns, qc, primers, dynamic. Another way to receive both lists is to add a non-existent or misspelled name to the list. The error message will then display all possible columns and categories.

Note that because of this feature the order of columns might be different compared to previous versions of Nextclade.

Add URL parameter for running analysis of example sequences

You can now launch the analysis of example sequences (as provided by the dataset) in Nextclade Web, by using the special keyword example in the input-fasta URL parameter. For example, navigating to this URL will run the analysis of example SARS-CoV-2 sequences (same as choosing "SARS-CoV-2" and then clicking "Load example" in the UI):

https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=example

This could useful for example for testing new datasets:

https://clades.nextstrain.org/?dataset-url=http://example.com/my-dataset-dir&input-fasta=example

Add index column to CSV and TSV outputs

The index field is already present in other output formats. In this version CSV and TSV output files gain index column as well, which contains the index (integer signifying location) of a corresponding record in the input fasta file or files. Note that this is not the same as row index, because CSV/TSV rows can be emitted in an unspecified order in Nextclade CLI (but this can be changed with --in-order flag; which is set by default in Nextclade Web).

Note that sequence names (seqName column) are not guaranteed to be unique (and in practice are not unique very often). So indices is the only way to reliably link together inputs and outputs.

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