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Given a set of strings, the shortest common superstring problem is to findthe shortest possible string that contains all the input strings. The problemis NP-hard, but a lot of work has gone into designing approximation algorithmsfor solving the problem. We present the first time and space efficientimplementation of the classic greedy heuristic which merges strings indecreasing order of overlap length. Our implementation works in $O(n \log\sigma)$ time and bits of space, where $n$ is the total length of the inputstrings in characters, and $\sigma$ is the size of the alphabet. After indexconstruction, a practical implementation of our algorithm uses roughly $5 n\log \sigma$ bits of space and reasonable time for a real dataset that consistsof DNA fragments.

Greedy Shortest Common Superstring Approximation in Compact Space