“…quality filtering/trimming, adapter removal, optional merging of forward and reverse reads), an optional plant host removal and/or assembly step, taxonomic classification of reads or contigs (mapping, sequence/domain similarity searches or k-mer based approaches against virus or more general databases) and finally -if necessary -haplotype reconstruction. Dedicated software combining all analyses steps exist, such as VirAnnot (Lefebvre et al, 2019), Virusdetect (Zheng et al, 2017), Virfind (Ho & Tzanetakis, 2014), Virtool (Rott et al, 2017), IDseq (Kalantar et al, 2020), Galaxy (Afgan et al, 2018 with for example Kodoja as plug-in (Baizan-Edge et al, 2019), Truffle (Visser et al, 2016), but also more general commercial software, such as CLC Genomics Workbench and Geneious Prime. Most of them aim to improve virus detection and/or reduce processing time, but the high number of pipelines available complicate the choice of the most appropriate for a given goal or environment.…”