Table 1 Sequencing library information and VEEV/EVEV detection information across various analytical tools from both virus-positive (4.1) and virus-negative (1.1) samples. Numbers in the rows corresponding to taxonomic analysis tools indicate the number of VEEV/EVEV reads detected by that tool from the particular dataset. Asterisks (*) indicate analysis against a curated database of 144 VEEV and EVEV genomes, rather than the full RefSeq-sized database used by kmer tools (Kraken, Kaiju, Centrifuge).
WTA Method | Illumina MiSeq Repli-G Nextera XT 2x150 P.E. | ONT MinION | ||||
|---|---|---|---|---|---|---|
Repli-G WTA | Sigma WTA | |||||
Library | 1D | 1D | ||||
NGS Method | R9.4 | R9.4 | ||||
Sample ID | 4.1 | 1.1 | 4.1 | 1.1 | 4.1 | 1.1 |
#Reads | 6,429,832 | 4,876,006 | 426,580 | 106,040 | 212,192 | 71,355 |
Avg. Length | 1,403 | 2,038 | 957 | 448 | ||
Max. Length | 21,358 | 61,951 | 13,207 | 60,685 | ||
VEEV Reads | ||||||
Kraken | 796 | 0 | 1 | 0 | 2 | 0 |
Kaiju | 2,420 | 0 | 10 | 0 | 17 | 1 |
centrifuge | 1,042 | 0 | 2 | 0 | 2 | 0 |
BWA MEM, default* | 5,269 | 0 | 27 | 0 | 21 | 6 |
BWA MEM -x ont2d* | — | — | 33 | 0 | 74 | 21 |
