3.11.0

3.11.0

Alignment presets

Nextclade CLI now supports --alignment-preset argument, which switches between pre-defined sets of alignment parameters. Currently available values are:

• default: Suitable for aligning very similar sequences (this is the default)
• high-diversity: Suitable for more diverse viruses
• short-sequences: Suitable for short and partial sequences

This is an experimental feature. Presets are subject to change.

Fix crash with empty reference sequence

Nextclade crashed when an empty reference sequence file is provided. Now Nextclade checks for this condition and reports a useful error message instead.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.