
Prokka Wishlist
---------------

* New --first-blast option, like --proteins?
* New --last-blast option eg. "nr" [Check who emailed me this]
* annotate possible frame-shifts
* FAQ about annotation transfer
* use included binary if PATH one is wrong version [Simon Gladman]
* reconsider !~m/a-z/ rule in cleanup_product() [Roderick Felsheim]
* all Kingdom=ALL or ANY for metagenomes [Andreas Bremges]
* make --cleanup option  for /product names [Andreas Bremges]
* locus_tag rules: http://www.ncbi.nlm.nih.gov/genomes/locustag/Proposal.pdf
* Bug: "existing RNA (repeat_region)" CRISPR is not RNA ?
* Factor out some functions into modules!
* Check for large genomic tracts which are unannotated. Sometimes Prodigal misses big genes.
* Add an example input/output so users can check their copy is producing similar results.
* Output potential homopolymer assembly errors near CDS flanks
* Add the CLUSTERS "PHA" library to Viruses mode.
* Option to include ribosomal binding sites (RBS) as features.
* Add hyperlinks to tool references in Manual

