What software to choose to do reference-assisted Birch Betula chloroplast genome assembly and subsequent annotation?

Question

[oxfordsoccer]

What software to choose to do reference-assisted Birch Betula chloroplast genome assembly and subsequent annotation?

I have tried de novo assembly using BBMap, NextGene`s DeBrujin with various k-mers, Flotton and PE Flotton, then run Prokka and RAST on the resultant contigs. Did not apply scaffolding and gap closure tools. Prokka annotated some genes, RAST could not annotate anything. Does anybody have an experience of a tree chloroplast genome assembly and annotation? Thx. You forum is a good help.

[Sej Modha]

IDBA-Hybrid is a good reference assisted genome assembly tool and if you haven't already tried it, RATT can be used for annotation transfer.

[h.mon]

I doubt Prokka and RAST will do a good job at annotating chloroplasts, you may try the tools listed here.