Software tools used in the workshop

Please see below the list of tools we have used and installed in the workshop VM.

We would highly recommend getting help from the appropriate IT/computing department to get these tools installed in your workplace.

Mikado - https://github.com/EI-CoreBioinformatics/mikado

Installation: https://github.com/EI-CoreBioinformatics/mikado#installation

Portcullis - https://github.com/EI-CoreBioinformatics/portcullis

Installation: https://github.com/EI-CoreBioinformatics/portcullis#installation

Minos - https://github.com/EI-CoreBioinformatics/minos

Installation: https://github.com/EI-CoreBioinformatics/minos#installation

We prefer users to use singularity container to install tools to avoid dependency issues that arise from different tools

Minos dependency tools, list here, can be installed using the singularity definition file provided here: https://github.com/EI-CoreBioinformatics/minos/blob/master/minos/etc/Singularity.tools.def

Once the dependencies are installed you can install Minos as per the instructions here: https://github.com/EI-CoreBioinformatics/minos#installation-from-github

Make sure we update the program_calls section of the run configuration file (etc/minos_config.yaml) https://github.com/EI-CoreBioinformatics/minos#registering-workflow-dependencies-with-minos, to point to the singularity container you have installed in your workplace

Minos requires Mikado and BUSCO to be installed as separate singularity images.

Mikado singularity definition file: You can use any one of the definition files that can be found here: https://github.com/EI-CoreBioinformatics/mikado/tree/master/Singularity

BUSCO singularity definition file: Please use the definition file that is provided here: https://github.com/EI-CoreBioinformatics/minos/blob/master/minos/etc/Singularity.busco.def

REAT - https://github.com/EI-CoreBioinformatics/reat

Prerequisites: https://github.com/EI-CoreBioinformatics/reat#prerequisites

Installation: https://github.com/EI-CoreBioinformatics/reat#installing

The majority of the tools we use in the workshop are installed as part of the REAT installation

The list of tools that are part of REAT installation, to name a few, is below:

DIAMOND
BioPerl
FullLengtherNext
BLAST
MagicBlast
LibDeflate
HTSLib
Samtools
BCFTools
BAMtools
gclib
gffread
GMAP
MiniMap2
GenomeTools
HISAT2
STAR
seqtk
Stringtie2
Scallop
Scallop-lr
Prodigal
Transdecoder
Portcullis
Mikado