PMC:7151644 / 7886-9042 JSONTXT

{"project":"2_test","denotations":[{"id":"32296543-31059795-144433899","span":{"begin":596,"end":600},"obj":"31059795"},{"id":"32296543-31059795-144433900","span":{"begin":896,"end":900},"obj":"31059795"},{"id":"32296543-20022975-144433901","span":{"begin":1127,"end":1131},"obj":"20022975"}],"text":"Bioinformatic analyses of the sequencing reads were undertaken as described previously (Shi et al. 2016a). In brief, adaptor- and quality-filtered sequencing reads were assembled de novo using the Trinity program (version 2.5.1). Viral contigs were identified by comparison (using blastn and Diamond blastx) to the NCBI non-redundant nucleotide (nt) and protein (nr) database with e-values set to 1 × 10−10 and 1 × 10−4, respectively. Likely contaminating viral sequences were excluded from the meta-transcriptomic data (Supplementary Table S2) using methods described previously (Asplund et al. 2019). In addition, the high frequency of retrovirus sequences was also excluded, as the majority of them probably were host genes, and some of them might be contaminating viral sequences, such as alpharetroviral and gammaretroviral sequences probably linked to laboratory components (Asplund et al. 2019). Finally, the putative viruses present in the blood, liver, spleen, lung, and kidney samples were confirmed by PCR. The quantity of the transcripts mapped to each viral contig was determined using the RSEM program (Li et al. 2010) implemented in Trinity."}