Welcome to the CTBMB Long Reads workshop
The instructions and code in this website are designed to be used along with our rstudio server.
Access the workshop rstudio server by going to rstudio.bioinformatics.guide
Use the links below to access notes for each section of the workshop. Keep the page open in a separate tab or window to allow you to cut and paste commands as you go.
- How to access the workshop server
- How to setup an RStudio project for taking notes
- Installing software with conda
- Locating minion output files
- Checking quality and quantity of data
- Trimming adapters
- Assembly with redbean
- Assembly with flye
- Comparison of assembly quality with QUAST
- Assembly polishing with medaka
- Annotation with prokka
- Aligning a repeat region back to the genome with minimap2
- Visualising genomic features with ggbio
- Aligning long-reads with minimap2
- Visualising read alignments with IGV