Automatically optimise three of Velvet's assembly parameters.

• Version: 2.2.6
• Added: March, 2022
• Link: https://github.com/tseemann/VelvetOptimiser

See which versions are available:

$ module avail velvetoptimiser

Load one version into your environment and run it:

$ module load velvetoptimiser/2.2.6
$ VelvetOptimiser.pl --help

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/tseemann/VelvetOptimiser/archive/refs/tags/2.2.6.zip
$ unzip 2.2.6.zip
$ cd VelvetOptimiser-2.2.6
$ grep -rh -oE "use Bio::.*$" VelvetOpt/* VelvetOptimiser.pl | sort -u | awk '{print $2}' | sed 's/;//'
Bio::SeqIO
$ cpanm -l perl5 Bio::SeqIO --force
$ sudo mkdir -p /export/apps/velvetoptimiser/2.2.6
$ sudo cp -r . /export/apps/velvetoptimiser/2.2.6

Note 1: VelvetOptimiser only says that it requires "BioPerl", but the BioPerl distribution frowns upon requiring the entire distribution. Here I have attempted to guess which modules are needed by checking the actual Perl "use" statements.