Fig. 1

Identification, serotyping and genome recovery of influenza A virus based on reads. Expected proportions of H1N1 within mixed RNA samples were 0.55 % (a, and c) and 1.5 % (b, and d). a and b Percentages of reads aligned to influenza A virus among all reads passing quality control. Black dashed lines denote expected proportion of influenza A virus. c and d Influenza A virus-aligned read distribution for influenza A viral RNA segments. Influenza A virus-aligned reads of “BD + WTA (8 h)” are insufficient; thus, their distribution is not shown. e Site depths based on NGS read alignments on eight H1N1 RNA segments are shown as a filled area graph, colored by experimental condition. Segment names and their positions are labeled at top and bottom, respectively. Assembled contig alignments are denoted by thick lines (Velvet assembly) or thin lines (Trinity assembly) up the site depth profiles. f H1N1 genome recovery coverage with increasing numbers of random sampling reads. For a given read number, influenza A virus-aligned reads were randomly sampled 10 times for de novo assembly, and the average coverage values are shown