Bioinformatic tools installation guides

Collection of instructions for installation of various bioinformatic tools.

Some categorisation and software list were borrowed from:

• Holland Computing Center
• Metagenomics.wiki
• The University of Texas in Austin
• Hummingbird Computational Cluster
• BioLinux

List of software in instructions

• Quality assessment of raw sequences:

  • FastQC
  • QUAST

• Annotation:

  • prokka

• Alignment tools:

  • BLAT
  • Bowtie / Bowtie2
  • Clustal Omega
  • TopHat2 (low maintenance, replaced by HISAT)
  • HISAT2 + genotype
  • BLAST2
  • Burrows-Wheeler Aligner (BWA)

• Data Manipulation Tools:

  • SRAtoolkit
  • BAMTools
  • SAMtools

• De novo assembly tools:

  • Abyss
  • Velvet + Oases
  • Ray
  • SOAPdenovo2
  • SOAPdenovo
  • SPAdes
  • QIIME II
  • TrinityRNAseq

• Pre-processing tools:

  • Cutadapt
  • PRINSEQ
  • PRINSEQ++
  • Scythe
  • Sickle
  • TagCleaner

• Reference based assembly tools:

  • Cufflinks

• Tools for removing / Detecting redundant sequences

  • CAP3
  • CD-HIT

• Taxonomic classification

  • GTDB-Tk

• General purpose tools:

  • BioPerl
  • BioPython
  • Bio++ Suite
  • Anaconda3

Remark regarding Ubuntu

NB! : When referring to Ubuntu, it refers to both native Ubuntu installation and Ubuntu running from under Windows

To install Ubuntu from under Windows 10:

1. Start button -> type Control Panel -> navigate to Programs and Features -> Click on Turn Windows Features on or off In the popped-up windows find Windows Subsystem for Linux checkbox and make sure it's checked.
2. Reboot Windows.
3. OPTIONAL:\

• If windows is not fully updated, it uses WSL 1, but WSL2 is more preferable. To force use of WSL2, open PowerShell and type wsl.exe --set-default-version 2
• after that update Windows 10, reboot may be required

4. Start button -> Type Microsoft Store -> Find Ubuntu or Ubuntu 20.04 LTS and install it.
5. To run Ubuntu: Start button -> type bash and hit Enter
6. There are issues with snapd running at WSL. Better to remove it: sudo apt remove snapd -y

To upgrade the Ubuntu on Windows 10 WSL (not from 20.04!)

1. Download and install WSL2 core update
2. Force use of WSL 2

• Open PowerShell and run wsl.exe --set-default-version 2

3. Convert the existing installation of Ubuntu to WSL2 :

• Open PowerShell and runwsl.exe --set-version Ubuntu 2

4. Update Windows 10 (reboot may be required)
5. run bash and perform:

• sudo apt remove snapd -y
• sudo apt update && sudo apt full-upgrade -y
• edit /etc/update-manager/release-upgrades file and make sure that line with Prompt= is Prompt=normal
• sudo do-release-upgrade -d

6. Restart the linux terminal

Environment Modules

Project Website | Github | Wikipedia

Environment Modules can be installed for:

• Ubuntu 20.04, 21.10:
  sudo apt install environment-modules -y
• Fedora 33:
  sudo dnf install environment-modules -y
• CentOS 8:
  sudo yum install environment-modules
• Arch:
  sudo pamac -S env-modules (not tested yet)