DeGeCI 1.1: a web platform for gene annotation of mitochondrial genomes

Abstract Summary DeGeCI is a command line tool that generates fully automated de novo gene predictions from mitochondrial nucleotide sequences by using a reference database of annotated mitogenomes which is represented as a de Bruijn graph. The input genome is mapped to this graph, creating a subgraph, which is then post-processed by a clustering routine. Version 1.1 of DeGeCI offers a web front-end for GUI-based input. It also introduces a new taxonomic filter pipeline that allows the species in the reference database to be restricted to a user-specified taxonomic classification and allows for gene boundary optimization when providing the translation table of the input genome. Availability and implementation The web platform is accessible at https://degeci.informatik.uni-leipzig.de. Source code is freely available at https://git.informatik.uni-leipzig.de/lfiedler/degeci.