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

• Version: 1.3.0
• Added: February, 2021
• Updated: September, 2021
• Link: https://github.com/nextstrain/nextclade/tree/master/packages/nextclade_cli

See versions of nextclade which are available:

$ module avail nextclade

Load one version into your environment and run it:

$ module load nextclade/1.3.0
$ nextclade

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/nextclade/1.3.0/bin
$ sudo wget https://github.com/nextstrain/nextclade/releases/download/1.3.0/nextclade-Linux-x86_64 -O /export/apps/nextclade/1.3.0/bin/nextclade
$ sudo chmod +x /export/apps/nextclade/1.3.0/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.