Assembly of chloroplast genome from plant WGS

Question

[adarsh_munna]

Hi,

I want to perform de novo assembly of chloroplast genome. However chloroplast enrichment was not performed during sequencing, so the final data contains the entire genome. Reference genome is not available for the plant sample. The samples are sequenced in Illumina.

I would like to know how can I specifically perform assembly chloroplast genome assembly from such WGS plant sample. I read through some tools like chloroExtractor, Fast-Plast, GetOrganelle, and NOVOPlasty. Will this tools be able to specifically identify the reads and assemble? Or is there a way to extract or identify the reads and then perform the chloroplast assembly?

Please suggest.

Thanks

[GenoMax]

Those tools should be able to do this as demonstrated by an example that uses a WGS dataset and GetOrganelle: https://github.com/Kinggerm/GetOrganelle/wiki/Example-3