Platform and data access
This workshop is designed to be conducted on the NeSI compute infrastructure. All software and data are already set up for you to use during the workshop.
Software
The software needed to run this lesson are listed below. Versions reported are the ones we use on NeSI but the lesson is likely to work with a range of versions of these softwares.
| Software | Version | Manual | Description | |
|---|---|---|---|---|
| Jellyfish | 2.3.0 | link | K-mer analysis | |
| FastQC | 0.11.9 | link | Illumina read QC | |
| SeqKit | link | |||
| NanoStat | 1.5.0 | link | Nanopore read QC | |
| nanofilt | 2.6.0 | link | Nanopore read filtering | |
| Flye | 2.9.1-b1780 | link | Long-read genome assembler | |
| BWA | 0.7.17 | link | Read mapping, assembly indexing | |
| medaka | 1.6.0 | link | Assembly polishing | |
| Pilon | 1.24 | link | Nanopore assembly polishing | |
| SAMtools | 1.15.1 | link | Read mapping | |
| QUAST | 5.2.0 | link | Assembly QC | |
| BUSCO | 5.1.3 | link | Assembly QC - gene orthologs | |
| KAT | 2.4.2 | link | K-mer based assembly QC |