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 on Fox.

Individual packages may be loaded with the following command (replace BWA/0.7.17-GCCcore-11.2.0 with the name of the required module):

module load BWA/0.7.17-GCCcore-11.2.0

All of these packages are part of the meta-package IN-BIOS5000/HT-2022 that may be loaded with the following command:

module load IN-BIOS5000/HT-2022

Below is a list of the packages that will be used.

Package	Version	Kind	Module	Documentation	Source code repository
assembly-stats	0.1.4	Python library	assembly-stats/0.1.4-foss-2021b-Python-3.9.6	https://pypi.org/project/assembly-stats	https://github.com/MikeTrizna/assembly_stats
BEDTools	2.30.0	Binary	BEDTools/2.30.0-GCC-11.2.0	https://bedtools.readthedocs.io/en/latest	https://github.com/arq5x/bedtools2
BWA	0.7.17	Binary	BWA/0.7.17-GCCcore-11.2.0	https://github.com/lh3/bwa	https://github.com/lh3/bwa
bwa-mem2	2.2.1	Binary	bwa-mem2/2.2.1	https://github.com/bwa-mem2/bwa-mem2	https://github.com/bwa-mem2/bwa-mem2
EIGENSOFT	7.2.1	Binary	EIGENSOFT/7.2.1-foss-2021b	https://github.com/DReichLab/EIG	https://github.com/DReichLab/EIG
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
FASTX-Toolkit	0.0.14	Binary	FASTX-Toolkit/0.0.14-GCC-11.2.0	http://hannonlab.cshl.edu/fastx_toolkit	https://github.com/agordon/fastx_toolkit
Flye	2.9.1	Binary	Flye/2.9.1-GCC-11.2.0	https://github.com/fenderglass/Flye	https://github.com/fenderglass/Flye
GATK	4.2.6.1	Java	GATK/4.2.6.1-GCCcore-11.2.0-Java-11	https://gatk.broadinstitute.org/hc/en-us	https://github.com/broadinstitute/gatk
MultiQC	1.12	Binary	MultiQC/1.12-foss-2021b	https://multiqc.info	https://github.com/ewels/MultiQC
Pilon	1.24	Java	Pilon/1.24-Java-11	http://software.broadinstitute.org/software/pilon	https://github.com/broadinstitute/pilon
PLINK	1.9b6	Binary	PLINK/1.9b_6.21-x86_64	https://www.cog-genomics.org/plink/1.9	https://www.cog-genomics.org/plink/1.9/dev
QUAST	5.2.0	Binary	QUAST/5.2.0-foss-2021b	http://cab.spbu.ru/software/quast	https://github.com/ablab/quast
SAMtools	1.15	Binary	SAMtools/1.15-GCC-11.2.0	https://www.htslib.org	https://github.com/samtools/samtools
SPAdes	3.15.5	Binary	SPAdes/3.15.5-GCC-11.2.0	http://cab.spbu.ru/software/spades	https://github.com/ablab/spades
Trimmomatic	0.39	Java	Trimmomatic/0.39-Java-11	http://www.usadellab.org/cms/?page=trimmomatic	https://github.com/usadellab/Trimmomatic
Unicycler	0.5.0	Binary	Unicycler/0.5.0-gompi-2021b	https://github.com/rrwick/Unicycler	https://github.com/rrwick/Unicycler
VCFtools	0.1.16	Binary	VCFtools/0.1.16-GCC-11.2.0	https://vcftools.github.io/index.html	https://github.com/vcftools/vcftools
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