3.12.0
3.12.0
Forbid reference sequences with gaps
Starting from this version, Nextclade won't accept reference sequences (reference.fasta) which contain gap characters (-).
This is true for reference sequences in Nextclade datasets (provided as --input-dataset, --dataset-name in CLI, or ?input-dataset, ?dataset-name in web), Auspice JSON datasets (through --input-dataset-json or ?input-dataset-json) as well as for individually provided reference sequences, in absence of a dataset or when overriding its files (--input-ref, ?input-ref).
We could not find meaning for the gaps in reference sequences in the context of Nextclade (pairwise alignment and comparison of sequences to a reference). When a reference with gaps have been used, it could have been causing errors and even possibly produced incorrect results silently.
Starting from this version, Nextclade will now stop with an explicit error if it detects gaps in reference sequence. To resolve, please use a reference sequence without gaps, if possible, or notify dataset authors about the problem.
If you think that Nextclade needs to support reference sequences with gaps please submit a new issue and explain your use-case and motivation on GitHub: https://github.com/nextstrain/nextclade/issues
Installation and usage📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI:
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