Table 3.
Mapping parameters used for finding chimeric reads with CLC genomics workbench 10. The reads used for these comparisons were produced using a sequencing read generator tool (ART_ILLUMINA v2.5.8).
| Tool parameters | CLC mapping | human reads-HPV references | HPV reads-human reference | |
|---|---|---|---|---|
| •match score = 1 | Gobal alignment | 90% identity | 4,572,369 (7.8%) | 1,448,604 (99.9%) |
| •mismatch cost = 2 | 40% length | |||
| •Linear gap cost of insertion/deletion | 90% identity | 4,576,999 (7.8%) | 1,448,607 (99.9%) | |
| •Insertion cost = 3 | 30% length | |||
| •Deletion cost = 3 | Local alignment | 90% identity | 10,226 (0.01%) | 6,365 (0.4%) |
| 40% length | ||||
| 90% identity | 49,806 (0.08%) | 17,688 (1.2%) | ||
| 30% length | ||||
| Total reads | 58,333,246 (human) | 1,448,670 (HPV) | ||