Skip to main content

Advertisement

Table 1 Genome de novo assembly

From: Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

Treatmenta Trinity assembler Velvet assembler IDBA-UD assembler
Contig total size (bp)b Genome coverage (%) H1 + N1 coverage (%) Contig total size (bp)b Genome coverage (%) H1 + N1 coverage (%) Contig total size (bp)b Genome coverage (%) H1 + N1 coverage (%)
BD (0.55 %)a 12,987 95.3 98.3 12,163 89.2 89.5 13,035 95.6 95.0
No pretreatment (0.55 %)a 13,351 97.9 98.5 12,993 95.3 96.5 13,077 95.9 95.5
BD + 8-h WTA (0.55 %)a
8-h WTA (0.55 %)a 12,912 94.7 97.3 12,649 92.8 90.9 10,723 78.7 83.8
BD + 2-h WTA (1.50 %)a 13,431 98.5 97.3 12,555 92.1 91.3 13,083 95.9 91.7
No pretreatment (1.50 %)a 13,461 98.7 98.5 13,064 95.8 99.6 13,240 97.1 94.4
  1. aExpected proportions of H1N1 within mixed RNA samples are indicated in parentheses
  2. bContigs generated by assemblers were aligned to the H1N1 reference genome. Contig total sizes were obtained from aligned contigs. Overlapping contig regions were counted only once