ZORRO is a tool for hybrid assembly that can combine Illumina and 454 contigs. The pipeline consists of repeat masking in contigs, detection of overlapping regions, unmasking repeats, and finally assembly of the contigs.
Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F, Costa GG, Vidal RO, Noronha MF, Dominska M, Andrietta MG, Andrietta SR, Cunha AF, Gomes LH, Tavares FC, Alcarde AR, Dietrich FS, McCusker JH, Petes TD, Pereira GA "Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production." Genome Res. 2009 Dec;19(12):2258-70. https://doi.org/10.1101/gr.091777.109
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