Table 1 An overview of the notation used in the paper

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, \(\mathsf{T}\backslash \mathsf{R}\) -