A simple R shiny app to visualize contigs, scaffolds, and telomere motifs.
You can test the app here: https://gbdias-teloview.share.connect.posit.cloud
Example of teloview output. Contigs are rendered as segments of alternating colors inside each scaffold. The abundance of the telomere motif is shown in the red line above each scaffold.
Tip
The Posit Cloud instance of this app is hosted on a free plan and might take a long time to launch. For more stable/quicker usability try cloning the repository and executing the app.R script locally. You will need to install : shiny, shinythemes, dplyr, karyoploteR, and rtracklayer for it to work.
- Assembly file in AGP/BED format
- Telomere track in bedGraph format
For a scaffolded assembly, it takes an AGP file as input, such as the output of Hi-C scaffolding with tools like YaHS. Alternatively, you can provide scaffold names and start and end coordinates in BED format (e.g. scaffold1 0 12000). In this case, only scaffolds will be drawn and no contig boundaries will be shown.
For the telomere track, a bedGraph file must be provided. This can be quickly generated with tidk as follows:
tidk search --string TTACC --output telo_track --dir ${PWD} --extension bedgraph
Make sure to replace the telomere string with the correct sequence for your species. Check TeloBase for a compilation of telomere sequences.