Table 1 User-specified parameters of CASPER and the default values used for experiments
From: CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing
Parameter | Default | Description |
|---|---|---|
K | 17 | The size of k-mers (in bp) used to represent contexts around mismatching bases |
Ω | 10 | The minimum length (in bp) of the overlap between forward and reverse reads |
γ | 0.5 | CASPER abandons merging if the mismatch ratio in the overlap is greater than γ |
δ | 19 | Context-based mismatch resolution starts if quality scores differ less than δ |