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 |