Table 3.

De Novo Assembly Tools Suitable for the Assembly of Viral Genomes

Tool	Description	Ref.
AV454	AV454 is a de novo consensus assembler designed for small and nonrepetitive genomes sequenced at high depth.	Henn et al. (2012)
RIEMS	RIEMS is a software for the sensitive and reliable analysis of metagenomic datasets.	Scheuch et al. (2015)
V-FAT	V-FAT is a tool to perform automated computational finishing and annotation of de novo viral assemblies.	Charlebois et al. (n.d.)
VICUNA	VICUNA is a de novo assembly tool targeting populations with high mutation rates.	Yang et al. (2012)
VrAP	The VrAP (Viral Assembly Pipeline) is based on the genome assembler SPAdes (Bankevich et al., 2012) combined with an additional read correction and several filter steps. The pipeline classifies the contigs (contiguous sequences constructed from short reads) to distinguish host from viral sequences. VrAP can identify viruses without any sequence homology to known references.	Fricke et al. (2017)