ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads Export

@article{citeulike:5871151, abstract = {We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8\% (ALLPATHS2), 68.7\% (Velvet), and 42.1 (EULER-SR).}, author = {MacCallum, Iain and Przybylski, Dariusz and Gnerre, Sante and Burton, Joshua and Shlyakhter, Ilya and Gnirke, Andreas and Malek, Joel and McKernan, Kevin and Ranade, Swati and Shea, Terrance and Williams, Louise and Young, Sarah and Nusbaum, Chad and Jaffe, David}, citeulike-article-id = {5871151}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2009-10-10-r103}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19796385}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19796385}, day = {1}, doi = {10.1186/gb-2009-10-10-r103}, issn = {1465-6906}, journal = {Genome Biology}, keywords = {assembly, bioinformatics, methods, shortread}, month = {October}, number = {10}, pages = {R103+}, posted-at = {2009-10-02 16:01:50}, priority = {2}, title = {ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads}, url = {http://dx.doi.org/10.1186/gb-2009-10-10-r103}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:5871151 L3 - citeulike-article-id:5871151 N2 - We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1 (EULER-SR). IS - 10 JF - Genome Biology SN - 1465-6906 TI - ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads VL - 10 SP - R103 KW - assembly KW - bioinformatics KW - methods KW - shortread AU - MacCallum, Iain AU - Przybylski, Dariusz AU - Gnerre, Sante AU - Burton, Joshua AU - Shlyakhter, Ilya AU - Gnirke, Andreas AU - Malek, Joel AU - McKernan, Kevin AU - Ranade, Swati AU - Shea, Terrance AU - Williams, Louise AU - Young, Sarah AU - Nusbaum, Chad AU - Jaffe, David PY - 2009/10/01/ UR - http://dx.doi.org/10.1186/gb-2009-10-10-r103 ER -