Table 1.

Bioinformatics tools for the identification of viruses in RNA-sequence samples.

Tool	Reference		Strategy	Benchmarking	Seq Input	Availability
VirFind	Ho and Tzanetakis, 2014	Web based tool that maps and removes host reads, gives taxonomic information for virus reads	Quality Control Mapping to host: Bowtie2 (Langmead, 2013) Assembly of non-host reads: Velvet Contigs compared with GenBank using Blastx Unmapped reads translated and compared against NCBI conserved domain database (Marchler-Bauer et al., 2015)	38 Plant samples from 19 species	sRNA mRNA	Web based tool with GUI http://virfind.org
Taxonomer	Flygare et al., 2016	Fast web-based metagenomics analysis tool based on k-mer profiling	Comprised of 4 modules Binner: compares reads to reference k-mer database [based on 21-kmers created using Kanalyze (Audano and Vannberg, 2014)] assigning to broad taxa (human, virus, bacteria) Classifier: exact k-mer matching within taxonomic bins against k-mer databases created from UniRef datasets (Suzek et al., 2015) (e.g., viral UniRef90) Protonomer: further classification in protein space AfterBurner: discovery of novel taxa	Human	mRNA	Webserver: https://www.taxonomer.com/
VSD toolkit	Barrero et al., 2017	Modules and workflows in the Yabi analytical environment for identification of viral sequences in plants	Quality Control De novo assembly: SPAdes (Bankevich et al., 2012) Overlapping contigs merged Contigs >40 nt aligned to plant, virus and viroid Genbank databases using Blastn and Blastx Unmapped contigs filtered and analyzed to identify putative circular viroids	21 Plant genomes	sRNA	Source code available to use with Yabi (Hunter et al., 2012) https://github.com/muccg/yabi
Metavisitor	Carissimo et al., 2017	Modular tools and workflows within the Galaxy analytical environment, designed for detection and reconstruction of viral genomes	Quality control Mapping to host, symbionts and parasites: Bowtie2 Unmapped reads assembled using Velvet + Oases (Schulz et al., 2012) or Trinity Contigs compared to Genbank virus database using Blastx and Blastn Blast guided scaffolding of selected virus sequences	Human Drosphila Mosquito	mRNA	Source code available to use within Galaxy (Afgan et al., 2016). Galaxy Toolshed: suite_metavisitor_1_2 Galaxy instance: https://mississippi.snv.jussieu.fr/
VIP	Li et al., 2016	An integrated pipeline for metagenomics of virus identification and discovery	Quality Control Mapping to host: Bowtie2 Fast Mode: reads mapped to Virus Pathogen Resource (ViPR) (Pickett et al., 2012) and Influenza Database (Squires et al., 2012) Sense mode: reads mapped to virus RefSeq (O'Leary et al., 2016) nucleotide Unmapped reads mapped to RefSeq protein: RAPSearch (Zhao et al., 2012) Options for de novo assembly with Velvet-Oases	Human	mRNA	Local Installation. Code available at https://github.com/keylabivdc/VIP
ViromeScan	Rampelli et al., 2016	Tool for metagenomics viral community profiling	Mapping to built-in databases (includes plants): Bowtie2 Mapped reads processed for quality Human Best Match Tagger (BMTagger) (Agarwala and Aleksandr, 2011) used to screen out human and bacterial sequences Screened reads re-mapped to virus database: Bowtie2	Human	mRNA	Local installation. Code available at http://sourceforge.net/projects/viromescan
VirusHunter	Zhao et al., 2013	Data analysis pipeline for novel virus identification from Roche 454 sequencers and other long read platforms	Similar reads clustered using CD-Hit (Li and Godzik, 2006) and longest sequence used as representative Repeat regions masked with Repeat Masker (Smit et al., 2013) Mapping to host (default: Human): Blastn Unmapped sequences aligned to NCBI nucleotide database and classified into taxonomies Unmapped sequences mapped to NCBI nr databases using Blastx	BHK (hamster) cell culture infected with viruses	mRNA	http://pathology.wustl.edu/VirusHunter/Code available upon request for local installation
ezVIR	Petty et al., 2014	Bioinformatics pipeline to evaluate spectrum of known human viruses	Mapping to host (Human genome): Bowtie2 Nonhost mapped to custom virus database: Bowtie2 Additional analysis on specific mapped classes provides targeted strain classification	Human	mRNA	Local installation. Code available: http://cegg.unige.ch/ezvir
Virus Detect	Zheng et al., 2017	Bioinformatics pipeline to analyse sRNA datasets for both known and novel virus identification	Maps reads to virus reference sequences: BWA Mapped reads assembled using references Mapped reads de novo assembled using Velvet Reference assemblies and de novo assemblies pooled and redundant sequences removed Contigs compared to virus reference nulcotides: Blastn Unmatched contigs matched to virus reference Blastx	Plants (Potato)	sRNA	Webserver: http://bioinfo.bti.cornell.edu/tool/VirusDetect
VirusFinder	Wang et al., 2013	Software for detection of viruses and their host integration sites	Mapping to host (Human genome): Bowtie2 Non-host reads mapped one of two virus databases (Hirahata et al., 2007; Bhaduri et al., 2012): Bowtie2 Mapped reads de novo assembled: Trinity Contigs mapped to virus database and human genome For specific virus of interest host integration sites are identified using BWA (Li and Durbin, 2009)	Human	RNA-seq WGS Targeted	https://bioinfo.uth.edu/VirusFinder/

References for databases and software with multiple entries in table: Genbank (Benson et al., 2013), Blastx and Blastn (Altschul et al., 1990), Velvet (Zerbino and Birney, 2008), Bowtie2 (Langmead, 2013), Trinity (Grabherr et al., 2011).