Readers interested in doing genome assembly with low memory will find the following two github repositories useful. They are related to Christina Boucher et al’s recent ‘variable-Order de Bruijn graphs’ paper, but research along the same line started a long time back. For example, check our Succinct de Bruijn Graphs from Tetsuo Shibuyas Group posted in 2012 and Alex Bowe’s Succinct de Bruijn Graphs.
1. Succinct Data Structure Library 2.0 (simongog/sdsl-lite) can be accessed here.
SDSL - Succinct Data Structure Library
What is it?
The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. Succinct data structures can represent an object (such as a bitvector or a tree) in space close the information-theoretic lower bound of the object while supporting operations of the original object efficiently. The theoretical time complexity of an operations performed on the classical data structure and the equivalent succinct data structure are (most of the time) identical.
2. Cosmo (alexbowe/cosmo) is a fast, low-memory DNA assembler using a succinct (variable order) de Bruijn graph and can be accessed here.
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