SOPRA is a tool for optimising scaffolding of contig assembly using paired reads. This tool is able to use sequencing data from both Illumina and SOLiD. The algorithm implemented is different from greedy algorithms and used an optimization strategy that addresses problems of very short reads and sequencing errors.
Dayarian A, Michael TP, Sengupta AM "SOPRA: Scaffolding algorithm for paired reads via statistical optimization." BMC Bioinformatics. 2010 Jun 24;11:345. https://doi.org/10.1186/1471-2105-11-345
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