Table 1. Examples of time and computer resources used by software dedicated to assembly and annotation.

SPAdes is an assembler designed for the assembly of small genomes using short reads. Smartdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. The REPET package is a software suite dedicated to detect, classify and annotate repeats. EuGene is an open integrative gene finder for eukaryotic and prokaryotic genomes. Processing time and RAM used will be affected by amount of input data, complexity of data, and genome size.

Reference Genome	Size	Software	Input (space used on disk)	CPU/RAM Available	Real time	Max RAM Used
							Aliivibrio wodanis	4 972 754 bp	SPAdes v3.10	200x Illumina reads (760 MB)	4 CPU/16GB RAM	2h17m3s	2,94GB
											12 CPU/256GB RAM	38m8s	9,37GB
							Caenorhabditis elegans	100 272 607 bp	Smartdenovo	20x Pacbio P6C4 Corrected long reads (1,9 GB)	8 CPU/16GB RAM	24m47s	1,92GB
80x Pacbio P6C4 Corrected long reads (7,6 GB)	8 CPU/16GB RAM	5h38m16s	7,29GB
REPET v2.5	C. Elegans genome (100 MB) Repbase aa 20.05 (20 MB) Pfam 27 (GypsyDB) (1,2 GB) rRNA from eukaryota (2,6 MB)	8 CPU/16 GB RAM	1h53m11s + 19h9m40s	8,96GB
Eugene v4.2a	C. Elegans genome (100 MB) Repbase aa 20.05 (20 MB) Proteins sequences (swissprot) (2,8 MB) ESTs sequences (29 MB)	8 CPU/32 GB RAM	5h2m30s	16,94GB
Arabidopsis thaliana	134 634 692 bp	Smartdenovo	20x Pacbio P5C3 corrected long reads (2,7 GB)	8 CPU/16GB RAM	1h16m20s	2,4GB
		REPET v2.5	A. Thaliana genome (130 MB) Repbase aa 20.05 (20 MB) Pfam 27 (GypsyDB) (1,2 GB) rRNA from eukaryota (2,6 MB)	8 CPU/16 GB RAM	5h6m23s + 33h10m34s	10,25GB
		Eugene v4.2a	A. Thaliana genome (130 MB) Repbase aa 20.05 (20 MB) Proteins sequences (swissprot) (9,2 MB) ESTs sequences (31 MB)	8 CPU/32 GB RAM	6h17m18s	17,25GB
Theobroma cacao	324 761 211 bp	Eugene v4.2a	T. Cacao genome (315 MB) Repbase aa 20.05 (20 MB) Proteins sequences (swissprot) (31 MB) ESTs sequences (103 MB)	8 CPU/188 GB RAM	41h27m13s	72,5GB