Hierarchical Scaffolding With Bambus Export

@article{pop:bambus, abstract = {10.1101/gr.1536204 The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. 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.}, address = {The Institute for Genomic Research (TIGR), Rockville, Maryland 20850, USA. mpop@tigr.org}, author = {Pop, Mihai and Kosack, Daniel S. and Salzberg, Steven L.}, citeulike-article-id = {1145127}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.1536204}, citeulike-linkout-1 = {http://genome.cshlp.org/content/14/1/149.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/14/1/149.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/14707177}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=14707177}, doi = {10.1101/gr.1536204}, issn = {1088-9051}, journal = {Genome Research}, keywords = {amos, scaffolding, thesis}, month = {January}, number = {1}, pages = {149--159}, posted-at = {2008-05-19 16:27:18}, priority = {3}, title = {Hierarchical Scaffolding With Bambus}, url = {http://dx.doi.org/10.1101/gr.1536204}, volume = {14}, year = {2004} }

TY - JOUR ID - pop:bambus L3 - citeulike-article-id:1145127 N2 - 10.1101/gr.1536204 The output of a genome assembler generally comprises a collection of contiguous DNA sequences (contigs) whose relative placement along the genome is not defined. A procedure called is commonly used to order and orient these contigs using paired read information. This ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. 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. IS - 1 JF - Genome Research SN - 1088-9051 AD - The Institute for Genomic Research (TIGR), Rockville, Maryland 20850, USA. mpop@tigr.org EP - 159 TI - Hierarchical Scaffolding With Bambus VL - 14 SP - 149 KW - amos KW - scaffolding KW - thesis AU - Pop, Mihai AU - Kosack, Daniel AU - Salzberg, Steven PY - 2004/01// UR - http://dx.doi.org/10.1101/gr.1536204 ER -