Table 5. Comparison of selected bacterial genome annotation pipelines.

Feature	Bacannot	Bactopia	ASA3P	MicrobeAnnotator	Nullarbor	TORMES
Sequence technology	Short and Long-reads	Short and Long-reads	Short and Long-reads	Short-reads	Short-reads
Assembly type	Short-reads, Long-reads and Hybrid	Short-reads and Hybrid	Short-reads, Long-reads and Hybrid	Paired-end short-reads only	Paired-end short-reads only
Single-end reads	Yes	Yes	Yes	No	No
Workflow	Nextflow	Nextflow	Groovy	Python	Perl + Make	Bash
Resume if stopped	Yes	Yes	No	Yes	Yes	No
Computing cluster and cloud compatibility	Yes	Yes	Yes	No	No	No
Batch processing from config file	Yes	Yes	Yes	Yes	Yes	Yes
Summary reports	HTML, Genome Browser and Shiny Application	Text	HTML	Text and Image	HTML	R Markdown
Package manager	Nextflow + Github	Nextflow + Conda	Conda	Conda and Brew	Conda
Container available	Yes	Yes	Yes	No	No	No
Documentation	Website and Readme	Website	PDF Manual and Readme	Readme	Readme	Readme
Source code	https://github.com/fmalmeida/bacannot	https://github.com/bactopia/bactopia	https://github.com/oschwengers/asap	https://github.com/cruizperez/MicrobeAnnotator	https://github.com/tseemann/nullarbor	https://github.com/nmquijada/tormes
Latest release (version/year)	v3.2/2022	v2.2.0/2022	v1.3.0/2020	v2.0.5/2021	v2.0.20191013/2019	v1.3.0/2021