Software used during the course
| Software | Version (if not latest) | Module | Notes |
|---|---|---|---|
| SPAdes | 4.0.0 | Assembly | |
| Flye | 2.9.4 | Assembly | |
| Unicycler | 0.5.1 | Assembly | |
| Snippy | 4.6.0 | Alignment/Variant calling | |
| Minimap2 | 2.28 (r1209) | Alignment | |
| DeepVariant | 1.6.1 | Variant calling | |
| PEPPER DeepVariant | r0.8 | Variant calling | |
| MultiQC | v1.23 | Accessing data and QC | |
| fastp | v0.23.4 | Accessing data and QC | |
| kraken2 | v2.1.3 | Accessing data and QC | |
| kraken2 database | Standard-8 | Accessing data and QC | |
| ABRicate | 1.0.0 | Detecting resistance using command line II | |
| Anaconda | Computing environment and set up | ||
| PointFinder | Detecting resistance using command line I | ||
| PointFinder DB | Detecting resistance using command line II | ||
| KMA | Detecting resistance using command line II | ||
| SNP-SITES | 2.5.1 | Analysing Phylogenetics | |
| IQTREE | 2.3.5 | Analysing Phylogenetics |
We are currently using Oracle VM Virtual Box (https://www.virtualbox.org/) to deliver Informatics, you can find Virtual Box Guides below:
Virtual Machine SetUp Guide for Intel-Mac and Windows.
The Host OS Requirements for Virtual Box
- RAM requirement: 8GB (preferably 12GB)
- Processor requirement: 4 processors (preferably 8)
- Hard disk space: 200GB
- Admin rights to the computer
Note: Please be aware that Virtual Box is currently incompatible with M1/M2/M3 chips on MacBook. It is exclusively designed for use on Intel-based MacBooks. The current version in use is Virtual Box 7.0.
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
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