Software that will be used in the course

Several software packages for general sequence handling, alignment, genome assembly, assembly quality assessment, and variant calling will be used during the course. They are available as software modules on Fox. The table below shows the packages that will be used.

Individual packages may be loaded with the following command (replace BWA/0.7.17-GCCcore-11.3.0 with the name of the required module):

module load BWA/0.7.17-GCCcore-11.3.0

The packages indicated with a ‘Yes’ in the first column in the table below are part of large meta module that may be loaded all together with this command:

module load IN-BIOS5000/HT-2024

The Flye, Velvet, MultiQC, and Unicycler modules can be loaded together simultaneously, but not at the same time as other modules.

The SAMtools and nf-core modules can not be loaded at the same time as other modules.

You may need to unload all or some modules in order to load other modules. All modules may be unloaded with the module purge command, and individual modules may be unloaded with the module unload command.

Meta	Package	Version	Kind	Module	Documentation	Source code repository
Yes	assembly_stats	0.1.4	Python library	assembly_stats/0.1.4-foss-2022a	https://pypi.org/project/assembly-stats	https://github.com/MikeTrizna/assembly_stats
Yes	BEDTools	2.30.0	Binary	BEDTools/2.30.0-GCC-11.3.0	https://bedtools.readthedocs.io/en/latest	https://github.com/arq5x/bedtools2
No	BCFtools	1.15.1	Binary	BCFtools/1.15.1-GCC-11.3.0	https://samtools.github.io/bcftools/bcftools.html	https://github.com/samtools/bcftools
Yes	BWA	0.7.17	Binary	BWA/0.7.17-GCCcore-11.3.0	https://github.com/lh3/bwa	https://github.com/lh3/bwa
Yes	EIGENSOFT	7.2.1	Binary	EIGENSOFT/7.2.1-foss-2022a	https://github.com/DReichLab/EIG	https://github.com/DReichLab/EIG
Yes	FastQC	0.11.9	Java	FastQC/0.11.9-Java-11	https://www.bioinformatics.babraham.ac.uk/projects/fastqc	https://github.com/s-andrews/FastQC
Yes	FASTX-Toolkit	0.0.14	Binary	FASTX-Toolkit/0.0.14-GCC-11.3.0	https://github.com/agordon/fastx_toolkit	https://github.com/agordon/fastx_toolkit
No	Flye	2.9.1	Binary	Flye/2.9.1-GCC-11.2.0	https://github.com/fenderglass/Flye	https://github.com/fenderglass/Flye
Yes	GATK	4.3.0.0	Java	GATK/4.3.0.0-GCCcore-11.3.0-Java-11	https://gatk.broadinstitute.org/hc/en-us	https://github.com/broadinstitute/gatk
No	MultiQC	1.12	Binary	MultiQC/1.12-foss-2021b	https://multiqc.info	https://github.com/ewels/MultiQC
Yes	Nextflow	24.04.2	Java	Nextflow/24.04.2	https://www.nextflow.io/docs/latest/index.html	https://www.nextflow.io/docs/latest/install.html
No	nf-core	2.13.1	-	nf-core/2.13.1-foss-2023b	https://nf-co.re/docs	https://nf-co.re/docs/nf-core-tools/installation
Yes	Pilon	1.24	Java	Pilon/1.24-Java-11	https://github.com/broadinstitute/pilon/wiki	https://github.com/broadinstitute/pilon
Yes	PLINK	2.00a3.7	Binary	PLINK/2.00a3.7-foss-2022a	https://www.cog-genomics.org/plink/2.0	https://www.cog-genomics.org/plink/2.0
Yes	QUAST	5.2.0	Binary	QUAST/5.2.0-foss-2022a	https://quast.sourceforge.net/docs/manual.html	https://github.com/ablab/quast
No	SAMtools	1.17	Binary	SAMtools/1.17-GCC-12.2.0	https://www.htslib.org	https://github.com/samtools/samtools
Yes	SPAdes	3.15.5	Binary	SPAdes/3.15.5-GCC-11.3.0	https://ablab.github.io/spades/	https://github.com/ablab/spades
Yes	Trimmomatic	0.39	Java	Trimmomatic/0.39-Java-11	http://www.usadellab.org/cms/?page=trimmomatic	https://github.com/usadellab/Trimmomatic
No	Unicycler	0.5.0	Binary	Unicycler/0.5.0-gompi-2021b	https://github.com/rrwick/Unicycler	https://github.com/rrwick/Unicycler
Yes	VCFtools	0.1.16	Binary	VCFtools/0.1.16-GCC-11.3.0	https://vcftools.github.io/index.html	https://github.com/vcftools/vcftools
No	Velvet	1.2.10	Binary	Velvet/1.2.10-GCC-11.2.0-mt-kmer_191	https://github.com/dzerbino/velvet	https://github.com/dzerbino/velvet