Fig. 1
From: viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data
Graphical representation of the viralFlye pipeline. viralFlye takes a set of long reads (ONT, CLC PacBio, or HiFi Pacbio) as an input and assembles them using metaFlye_v. If short reads are available, they are used for polishing the metaFlye assembly with freebayes [36] and bcfconsensus [38]. Afterward, viralFlye extracts short (length 5kb–1Mb) and high-coverage (coverage > 10x) isolated contigs as well as small multi-edge connected components. It further analyzes them and identifies putative MAVs using viralVerify and viralComplete and classifies the inferred MAVs into linear and circular using the CircularDisconnector module. Finally, it performs a CRISPR-based prediction of the virus-host associations (optional step)