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Most recent assemblers include a scaffolding module; however, users have little control over the scaffolding algorithm or the information produced. We thus developed a general-purpose scaffolder, called Bambus, which affords users significant flexibility in controlling the scaffolding parameters. Bambus was used recently to scaffold the low-coverage draft dog genome data. Most significantly, Bambus enables the use of linking data other than that inferred from mate-pair information. For example, the sequence of a completed genome can be used to guide the scaffolding of a related organism. We present several applications of Bambus: support for finishing, comparative genomics, analysis of the haplotype structure of genomes, and scaffolding of a mammalian genome at low coverage. Bambus is available as an open-source package from our Web site.<\/jats:p>","DOI":"10.1101\/gr.1536204","type":"journal-article","created":{"date-parts":[[2004,1,5]],"date-time":"2004-01-05T22:39:03Z","timestamp":1073342343000},"page":"149-159","source":"Crossref","is-referenced-by-count":172,"title":["Hierarchical Scaffolding With Bambus"],"prefix":"10.1101","volume":"14","author":[{"given":"Mihai","family":"Pop","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel S.","family":"Kosack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven L.","family":"Salzberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2004,1,5]]},"reference":[{"key":"2021111810533816000_14.1.149.1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1072104"},{"key":"2021111810533816000_14.1.149.2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.208902"},{"key":"2021111810533816000_14.1.149.3","doi-asserted-by":"crossref","unstructured":"Beigel, R., Alon, N., Apaydin, M.S., Fortnow, L., and Kasif, S. 2001. 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