Table 1.

Genome annotation pipelines

Pipeline name	Details	Source	URL
PGAP	An automatic prokaryotic genome annotation pipeline, which is a set of computational tools and algorithms that are used to predict the presence and location of genes in the genome of a prokaryotic organism	[63]	https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
Prokka v1.14.6	A software tool for rapidly annotating genomes, which uses external feature prediction tools like RNAmmer and Prodigal to identify the coordinates of genomic features within contigs	[61]	https://github.com/tseemann/prokka
RAST	A fully automated pipeline for annotating bacterial and archaeal genomes	[10]	https://rast.nmpdr.org/
MicrobeAnnotator	A tool that predicts all types of prokaryotic genes from a single or a set of anonymous genomic sequences of varying lengths. This tool is commonly used in the analysis of prokaryotic genomes	[58]	https://github.com/cruizperez/MicrobeAnnotator
EggNOG-mapper v2.1.9	A tool for automatically annotating the function of genes based on precomputed orthology assignments	[13]	http://eggnog-mapper.embl.de/
DRAM	A tool that uses databases like KEGG and PFAM to organize microbial genomic information into a catalog of microbial traits	[62]	https://github.com/WrightonLabCSU/DRAM
DFAST	A pipeline that supports genome submission to the public database DNA Data Bank of Japan (DDBJ) using the GHOSTX algorithm	[67]	https://dfast.ddbj.nig.ac.jp/
GenSAS	An online pipeline that provides structural and functional annotations of genomic sequences	[28]	https://www.gensas.org/
BlastKOALA	A tool that carries out automated annotation of fully sequenced genomes by using KEGG's internal annotation tool, KOALA, to assign K numbers to KEGG genes using SSEARCH computation	[33]	https://www.kegg.jp/blastkoala/