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Here is a list of software that is used in the practicals

Mapping

Software Notes
bwa Used for aligning short read data (e.g. Illumina)
minimap2 Used to align long read data (e.g. ONT)

Variant detection

Software Notes
bcftools
gatk Doesn't work on long read data
freebayes

Assembly

Software Notes
spades Only works on short read data
flye Assembly for long read data