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

Table 1 Genome de novo assembly

Treatment^a	Trinity assembler			Velvet assembler			IDBA-UD assembler
Treatment^a	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

^aExpected proportions of H1N1 within mixed RNA samples are indicated in parentheses
^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

ISSN: 1745-6150