A Fast Hybrid Short Read Fragment Assembly Algorithm Export

@article{citeulike:4920072, abstract = {Summary: The shorter and vastly more numerous reads produced by second-generation sequencing technologies require new tools that can assemble massive numbers of reads in reasonable time. Existing short-read assembly tools can be classified into two categories: greedy extension-based and graph-based. While the graph-based approaches are generally superior in terms of assembly quality, the computer resources required for building and storing a huge graph are very high. In this paper, we present Taipan, an assembly algo-rithm which can be viewed as a hybrid of these two approaches. Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make bet-ter decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources. Availability and Implementation: Source code in C running on Linux is freely available at http://taipan.sourceforge.net Contact: asbschmidt@ntu.edu.sg 10.1093/bioinformatics/btp374}, author = {Schmidt, Bertil and Sinha, Ranjan and Beresford-Smith, Bryan and Puglisi, Simon J.}, booktitle = {Bioinformatics}, citeulike-article-id = {4920072}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp374}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/17/2279.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/17/2279.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/17/2279}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19535537}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19535537}, day = {17}, doi = {10.1093/bioinformatics/btp374}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {analysis, genomics, sequencing, software}, month = {June}, number = {17}, pages = {btp374--2280}, posted-at = {2009-08-20 19:04:54}, priority = {2}, title = {A Fast Hybrid Short Read Fragment Assembly Algorithm}, url = {http://dx.doi.org/10.1093/bioinformatics/btp374}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4920072 L3 - citeulike-article-id:4920072 N2 - Summary: The shorter and vastly more numerous reads produced by second-generation sequencing technologies require new tools that can assemble massive numbers of reads in reasonable time. Existing short-read assembly tools can be classified into two categories: greedy extension-based and graph-based. While the graph-based approaches are generally superior in terms of assembly quality, the computer resources required for building and storing a huge graph are very high. In this paper, we present Taipan, an assembly algo-rithm which can be viewed as a hybrid of these two approaches. Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make bet-ter decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources. Availability and Implementation: Source code in C running on Linux is freely available at http://taipan.sourceforge.net Contact: asbschmidt@ntu.edu.sg 10.1093/bioinformatics/btp374 IS - 17 JF - Bioinformatics SN - 1460-2059 EP - 2280 TI - A Fast Hybrid Short Read Fragment Assembly Algorithm VL - 25 T2 - Bioinformatics SP - btp374 KW - analysis KW - genomics KW - sequencing KW - software AU - Schmidt, Bertil AU - Sinha, Ranjan AU - Beresford-Smith, Bryan AU - Puglisi, Simon PY - 2009/06/17/ UR - http://dx.doi.org/10.1093/bioinformatics/btp374 ER -