framefix | FastA DNA genome file 's ORFs to correct frameshifts

framefix is a Perl library. framefix has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Adjust a FastA DNA genome file's ORFs to correct frameshifts by best Diamond match. This is a simple script that corrects homopolymer stretches (e.g. GGGGGGGG) that putatively cause artifactual frameshifts in open reading frames of a prokaryotic genome. These false positive frameshifts are common in nanopore-derived genome assemblies, and the threshold for detection is based on that chemistry (homopolymers of 6bp+ for pore type R9.4). Frameshifts are corrected parsimoniously by adding or subtracting one base to restore the frame described by the best [Diamond] match against a provided protein database. The exception is if the parsimonious edit makes the homopolymer less than 6bp, in which case two bases are added to the homopolymer stretch to restore the reading frame. I would suggest running this script after other polishing methods such as nanopolish or Medaka.