Clade assignment, mutation calling, and sequence quality checks. This is the command line version of nextclade.

• Version: 2.11.0
• Added: February, 2021
• Updated: February, 2023
• Link: https://github.com/nextstrain/nextclade

See versions which are available:

$ module avail nextclade

Load one version into your environment and run it:

$ module load nextclade/2.11.0
$ nextclade

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/nextclade/2.11.0/bin
$ sudo wget https://github.com/nextstrain/nextclade/releases/download/2.11.0/nextclade-x86_64-unknown-linux-gnu -O /export/apps/nextclade/2.11.0/bin/nextclade
$ sudo chmod +x /export/apps/nextclade/2.11.0/bin/nextclade

Note: nextclade was previously distributed as a Javascript program, but it seems to have been ported to C++ and is now a standalone executable.