Sratoolkits

Installed latest release via git clone.

BLAST

The command line version of BLAST - officially referred to as ncbiblast - was installed directly from the NCBI website.

Diamond

Pre-compiled build of the most recent version of Diamond was installed from the GitHub repository.

FastQC/Multiqc

Load FastQC with Spack by using spack load [email protected]%[email protected]. Load MultiWC with Spack by using spack load [email protected]%[email protected].

Skewer

Installed latest release via git clone.

NGSComposer

Installed latest release via git clone.

Trimmomatic

Installed version 0.39 as a binary file from here.. As usual I merged the adapter files into a single file; since this is in root access only I used sudo sh -c 'cat * > all.fa' to merge the adapter files. Be sure to fix the resulting file if there are no newlines between sequences.

STAR

Installed latest release via git clone. I created symbolic links to the STAR executables we will be running within the main STAR directory:

cd STAR/
sudo ln -s ./bin/Linux_x86_64/STAR
sudo ln -s ./bin/Linux_x86_64/STARlong

Minimap2

Installed latest release via git clone. The executable needs to be created by running sudo make.

Burrow-Wheeler Aligner (BWA)

Installed latest release via git clone. The executable needs to be created by running sudo make.

HTSeq

Load HTSeq with Spack by using spack load [email protected]%[email protected].

samtools/bcftools/htslib

The latest releases of all three files were obtained from here.

Picard

Pre-compiled build of the most recent version of Picard was installed from the GitHub repository.

Freebayes

Installed latest release via git clone. This uses the Meson building system and requires ninja to create the files, so there are some additional requirements I needed to install (cmake, liblzma, etc.)