Author: Niccolo Alfano; Anisha Dayaram; Jan Axtner; Kyriakos Tsangaras; Marie-Louise Kampmann; Azlan Mohamed; Seth Timothy Wong; M. Thomas P. Gilbert; Andreas Wilting; Alex Daivd Greenwood
Title: Non-invasive surveys of mammalian viruses using environmental DNA Document date: 2020_3_29
ID: nil1vv6h_40
Snippet: Bacteriophages, invertebrate viruses and retroviruses were excluded from subsequent steps, which only focused on eukaryotic, specifically vertebrate viruses. The results of the three methods were compared and the viral contigs obtained were manually inspected. If more than one method generated a contig with the same viral hit, the contigs from each method were compared. If they had the same sequence or were overlapping, the longest contig was sel.....
Document: Bacteriophages, invertebrate viruses and retroviruses were excluded from subsequent steps, which only focused on eukaryotic, specifically vertebrate viruses. The results of the three methods were compared and the viral contigs obtained were manually inspected. If more than one method generated a contig with the same viral hit, the contigs from each method were compared. If they had the same sequence or were overlapping, the longest contig was selected. The filtered reads were mapped to the viral contigs to calculate the number of viral reads for each virus. Finally, the viral contigs were mapped to the reference genome of the virus corresponding to the best BLAST hit using Geneious v11.0.2 (Biomatters, Inc.) [43] . The baits were mapped to the same references to determine the genomic positions targeted by our bait panel for each virus.
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