Sanrrone / plotMyGBK

Plot your gbk in an standard circular plot.

plotMyGBK

---

plotMyGBK is a easy to use tool that use a genbank file to retrieve you a nice circular chart

Output example

Requisites

• Python 2.7 with biopython and pandas modules.
• R (tested in 3.2.3), and the following libraries:
  • Rsamtools
  • OmicCircos
  • data.table

Usage

plotMyGBK have minimal use:

python plotMyGBK.py -g mygenbank.gbk

and a complete use:

python plotMyGBK.py -g mygenbank.gbk -c annotationFile.tsv -w 3000 -s 1500 -l 500

• -g is the genbank file
• -c annotation file from prokka that contain the COG annotation (or something with that format).
• -w Windows size, to computing GC content and GC skew set the windows size, default:3000
• -s Step size, size in bp to move windows (-w), default:1500
• -l Filter Contigs, show only contigs that have more than 500bp

Output

Since your gbk, plotMyGBK will generate a folder called results_GBKNAME.faa where GBKNAME is the genbank file, this folder contain several files like faa, fna, parsed rpsblast results, other files necessaries to plot and last the plot in pdf format.

References

• Ying Hu Chunhua Yan [e-mail] (2015). OmicCircos: High-quality circular visualization of omics data. R package version 1.8.1.

Warning

• The script will plot at least all contigs, this is ideal for prokaryotes gbk files where there are few contigs (~100 or less), more than that might not look nicely.