Arche: An Advanced Flexible Tool for High-throuput Annotation of Functions on Microbial Contigs

Abstract

The growing amount of genomic data has prompted a need for less demanding and user friendly functional annotators. At the present, its hard to find a pipeline for the annotation of multiple functional data, such as both enzyme commission numbers (E.C.) and orthologous identifiers (KEGG and eggNOG), protein names, gene names, alternative names, and descriptions. In this work, we provide a new solution which combines different algorithms (BLAST, DIAMOND, HMMER3) and databases (UniprotKB, KOfam, NCBIFAMs, TIGRFAMs, and PFAM), and also overcome data download challenges. The software framework, Arche, herein demonstrated competitive results over Escherichia coli K-12 genome, the metagenome-assembled genome of Ferrovum myxofaciens S2.4, and a freshwater metagenome when compared to other annotators. Finally, Arche provides an analysis pipeline that can accommodate advanced tools in a unique order, creating several advantages regarding to other commonly used annotators.