symbols | meaning |
---|---|
A, B | genomic sequences |
\(R_{A}, R_{A}'\) (\(R_{B},R_{B}'\)) | read bags sequenced from A (B) |
a, b | a read from \(R_{A}\) (\(R_{B}\)) |
\(C_{A}\) (\(C_{B}\)) | contig set for A (B) assembled from \(R_{A}\) (\(R_{B}\)) |
\(\alpha\) (\(\beta\)) | a contig from \(C_{A}\) (\(C_{B}\)) |
\(\alpha ^{*}\) (\(\beta ^{*}\)) | a substring of contig \(\alpha\) (\(\beta\)) |
\(T_{A}\) (\(T_{B}\)) | \(R_{A}, C_{A}\) (\(R_{B}, C_{B}\)) tuple |
\(\mathsf{dist}(\cdot ,\cdot )\) | Levenshtein distance function |
\(\mathsf{dist}_{xy}(\cdot ,\cdot )\) | auxiliary (non-Levenshtein) distance functions, x, y indicate the respective argument types: \(\mathsf{r}\) - read, \(\mathsf{c}\) - contig, \(\mathsf{R}\) - read bag, \(\mathsf{C}\) - contig set, \(\mathsf{T}\) - read-contig tuple, \(\mathsf{T}\backslash \mathsf{R}\) - |