This is an old revision of the document!
Clade assignment, mutation calling, and sequence quality checks. This is the command line version of nextclade.
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.