Similar protocols

Pipeline publication

[…] 8, KR816220, KR816221 (fur seal parvoviruses); KR106199-KR106202, KR816213, KR816215, KR337994 (fur seal picornaviruses); KR072975-KR072979, KR072981, KR072982, KR072984 (fur seal sakobuvirus); KR106194-KR106196, KR106198, KR816216 (fur seal picobirnavirus); KR072985-KR072990 (fur seal rotavirus), KR827461 (fur seal hepevirus); KR072992, KR072994, KR072995 (fur seal sapovirus). The sequence data obtained from this study is available at the NIH Sequence Read Archive (SRA) under the study accession number SRP070196., Nucleotide or translated amino acid sequences from the contigs of anellovirus, parvovirus, picornavirus, picobirnavirus, rotavirus, sapovirus and hepevirus-like were aligned with MUSCLE (www.drive5.com/muscle) and phylogenetic trees were built using MEGA6 []. Trees were constructed by the neighbor-joining (NJ) method [] with a bootstrap of 1000 replicates, p-distance model, and gaps were treated as pairwise deletion. The contig sequences from this study were compared with other selected gene sequences available in the GenBank., A substantial proportion of the assembled reads detected in both fur seals species have no significant similarity to any of the sequences deposited to date at GenBank. About 70% of the assembled reads from the Ion Torrent platform had no significant hits, whereas in Illumina NGS apparatus the sequences with no identified matches reached 35% (cutoff for significant as <1e-05 BLASTx E score). The same divergence was observed with the number of bacterial hits, however, Ion Torrent had the lowest number of hits (about 25%) when compared to Illumina (about 60%)., The viral component detected in either of the sequencing platforms represented 4–5% of total sequences, regardless of the fur seal species analyzed. Most of the viral hits were from bacteriophages, in agreement with previous studies of bats and dromedary fecal viromes [–]. Some of the contigs from eukaryotic viruses displayed low similarity to currently known viruses and, as such, may represent novel viruses. The Subantarctic fur seal was found to carry a larger proportion of identifiable sequences of eukar […]

Pipeline specifications

Software tools MUSCLE, MEGA, BLASTX