Figure 5
From: PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
PACIFIC, BWA-MEM and Kraken2 virus predictions in RNA-seq data. Transparent grey filled circles represent detection thresholds for each class, overlaid with black filled circles representing the percentage of predicted reads using PACIFIC (left panel), BWA-MEM (centre panel) and Kraken2 (right panel). Circles are filled blue when the percentage of reads for a class are above detection thresholds described in Table 2. RNA-seq samples (y-axis) are labelled with NCBI SRA run accessions and abbreviations for sample type. (a) RNA-seq samples predicted to be positive for at least one viral class by PACIFIC, BWA-MEM, or Kraken2. Samples include a SARS-CoV-2-infected human patient bronchoalveolar lavage fluid sample (.pat), four in vitro SARS-CoV-2-infected NHBE cell lines (.scc) and 9 samples from the GALA II cohort (.gala). (b) Human RNA-seq samples without expected viral infections (.neg; n = 10). Samples were selected from the NCBI SRA database with no recorded evidence of infection.
