Table 1 General Assembly Statistics
From: Benchmarking different approaches for Norovirus genome assembly in metagenome samples
Sample A | Sample B | Sample C | Sample D | Sample E | Sample F | Sample G | Sample H | Average | |
|---|---|---|---|---|---|---|---|---|---|
Total number of reads | 68.7 M | 15.6 M | 47.3 M | 35.5 M | 23.1 M | 45.4 M | 45.3 M | 44.1 M | 40.6 M |
Ct value qRT-PCR | 25.1 | 21.38 | 26.3 | 13.91 | 13.91 | 24.3 | 21.6 | 23.9 | - |
%Total NoV reads (paired, unique reads mapping norovirus) | 18.5 | 15.6 | 1.4 | 93.9 | 34.4 | 42.9 | 98.6 | 76.5 | 47.7 |
%Total number of reads not mapping hs37d5 | 60.5 | 80.6 | 76 | 78.2 | 80 | 66.1 | 68.9 | 71.7 | 72.75 |
Completeness | YES | YES | YES | YES | YES | YES | YES | YES | - |
Mean coverage depth against final contigs | 453.05x | 2690.55x | 2587.67x | 7671.9x | 6309.99x | 7712.23x | 7805.97x | 7743.57x | 5371.87x |
% of total reads identified by mapping (final contig) | 0.026 | 15.79 | 1.43 | 94.31 | 34.32 | 42.97 | 98.77 | 76.93 | 45.57 |
Genotype | GII.17[P17] | GII.2[P2] | GII.17[P17] | GII.17[P17] | GII.17[P17] | GII.4[P4] | GII.4[P31] | GII.4[P4] | - |
Final contig length (bp) | 7551 | 7548 | 7560 | 7594 | 7589 | 7620 | 7674 | 7634 | - |
Published genomes assembly strategy+ | pC SPAdes | pC MEGAHIT | pD SPAdes | pD MEGAHIT | pD MEGAHIT | pD MEGAHIT | pD MEGAHIT | pD MEGAHIT | - |
% identity final contig against closest RefSeq reference* | 99.6 | 98.6 | 99.6 | 99.5 | 98.5 | 98.1 | 98.5 | 98 | - |
number total variants above 1 % against final genome | 230 | 180 | 187 | 15 | 55 | 43 | 23 | 32 | 95.6 |