Author: Conceição-Neto, Nádia; Theuns, Sebastiaan; Cui, Tingting; Zeller, Mark; Yinda, Claude Kwe; Christiaens, Isaura; Heylen, Elisabeth; Van Ranst, Marc; Carpentier, Sebastien; Nauwynck, Hans J.; Matthijnssens, Jelle
Title: Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs Document date: 2017_9_8
ID: kgoczioe_13
Snippet: Raw reads were filtered and trimmed for quality and adapters using Trimmomatic (Bolger et al. 2014 ) and assembled using SPAdes assembler version 3.5.0 (Bankevich et al. 2012) . Scaffolds were taxonomically classified using DIAMOND (sensitive option) (Buchfink et al. 2015) . ORFs were identified with ORF Finder analysis tools, Pfam was used to help predict enterovirus proteins and HMMER to infer insertion similarities (Zhang and Wood 2003; Finn e.....
Document: Raw reads were filtered and trimmed for quality and adapters using Trimmomatic (Bolger et al. 2014 ) and assembled using SPAdes assembler version 3.5.0 (Bankevich et al. 2012) . Scaffolds were taxonomically classified using DIAMOND (sensitive option) (Buchfink et al. 2015) . ORFs were identified with ORF Finder analysis tools, Pfam was used to help predict enterovirus proteins and HMMER to infer insertion similarities (Zhang and Wood 2003; Finn et al. 2011) . Amino-acid alignments of the viral sequences were performed with MUSCLE implemented in MEGA6.0 (Edgar 2004) . Substitution models for maximum likelihood phylogenetic trees were calculated using MEGA6.0 (Tamura et al. 2013) , and the appropriate best substitution model (with the lowest AIC) was used to build phylogenetic trees with 500 bootstrap replicates.
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