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Figure 3 | BMC Bioinformatics

Figure 3

From: Querying large read collections in main memory: a versatile data structure

Figure 3

Comparing the complexities of the Gk arrays and generalized Suffix Array based solutions. Comparing the complexities of Gk arrays and of the generalized Suffix Array solutions. A complexity is an expression that evaluates the running time or memory usage in function of parameters describing the input size. The construction time and space complexities of the index for q reads of length m having distinct k-mers are given for the generalized SA in (a), and for the Gk arrays in (b). We detail the cumulative space complexity during the construction of the gSA, and after the main steps of the construction algorithms. I.e.: once the gSA, the ISA, and the LCP arrays are built in (a), and once GkSA, GkIFA, and GkCFPS are built in (b). In (c) we give the time complexities for answering queries Q1-Q7 with a k-mer denoted by f. The procedures for the gSA depends on occ_C R (f), the occurrence number of f in the text made by the concatenation of all reads (i.e. in C R ), while those for the Gk arrays depends on occ_Reads(f), the occurrence number of f in all reads, and we know that occ_Reads(f)occ_C R (f).

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