# Workshop in Genomics - software and data - Marcela Uliano-Silva

| Software | version | link or instruction |
| -------- | -------- | -------- |
| Hifiasm | 0.19.5-r587 | installed with conda |
| FastK | latest | https://github.com/thegenemyers/FASTK |
| GENESCOPE.FK | latest | https://github.com/thegenemyers/GENESCOPE.FK/tree/main |
| perl | v5.26.1 | |
| python | 3.11 |conda |
|biopython | 1.81 |conda |
| matplolib matplolit-base | 3.7.1 | conda |
| asmstats | latest | https://github.com/marcelauliano/Teaching/blob/main/asmstats |
| MitoHiFi | latest, docker | https://github.com/marcelauliano/MitoHiFi/pkgs/container/mitohifi |
| singularity | =>3.7||
| awk ||
| seqtk | 1.3 | conda |
| plot_fasta_length.py | latest | https://github.com/marcelauliano/phython_scripts/blob/master/plot_fasta_length.py |

## I FORGOT TO INCLUDE BANDAGE!!!!

Data

| File | Link |
| -------- | -------- |
| PacBio large Dataset | https://darwin.cog.sanger.ac.uk/ilAgrStra1_PacBioHiFi_filtered.fasta.gz |
| Small Pacbio Dataset | https://darwin.cog.sanger.ac.uk/PacBioHiFi_100.fa.gz |
| Results folder | https://darwin.cog.sanger.ac.uk/Results.tar.gz |
|half pacbio file | https://darwin.cog.sanger.ac.uk/ilAgrStra1_PacBioHiFi_filtered.0.5.fasta.gz |
| second results folder | /Users/mu2/Google Drive/My Drive/Sanger/workshopGen2023/reduced/Results_05.tar.gz |