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 |