Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads Export

@article{citeulike:3339876, abstract = {Recent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa , strain PAb1, using very short read technology. From 8,627,900 reads, each 33 nucleotides in length, we assembled the genome into one scaffold of 76 ordered contiguous sequences containing 6,290,005 nucleotides, including one contig spanning 512,638 nucleotides, plus an additional 436 unordered contigs containing 416,897 nucleotides. Our method includes a novel gene-boosting algorithm that uses amino acid sequences from predicted proteins to build a better assembly. This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species.}, author = {Salzberg, Steven L. and Sommer, Daniel D. and Puiu, Daniela and Lee, Vincent T.}, booktitle = {PLoS Comput Biol}, citeulike-article-id = {3339876}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000186}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18818729}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18818729}, day = {26}, doi = {10.1371/journal.pcbi.1000186}, issn = {1553-7358}, journal = {PLoS Comput Biol}, keywords = {2gst, mapped\_assembly, prok-seq-cg-pipeline, scaffolding}, month = {September}, number = {9}, pages = {e1000186+}, posted-at = {2009-07-10 12:51:24}, priority = {2}, publisher = {Public Library of Science}, title = {Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000186}, volume = {4}, year = {2008} }

TY - JOUR ID - citeulike:3339876 L3 - citeulike-article-id:3339876 N2 - Recent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa , strain PAb1, using very short read technology. From 8,627,900 reads, each 33 nucleotides in length, we assembled the genome into one scaffold of 76 ordered contiguous sequences containing 6,290,005 nucleotides, including one contig spanning 512,638 nucleotides, plus an additional 436 unordered contigs containing 416,897 nucleotides. Our method includes a novel gene-boosting algorithm that uses amino acid sequences from predicted proteins to build a better assembly. This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species. IS - 9 JF - PLoS Comput Biol SN - 1553-7358 TI - Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads PB - Public Library of Science VL - 4 T2 - PLoS Comput Biol SP - e1000186 KW - 2gst KW - mapped_assembly KW - prok-seq-cg-pipeline KW - scaffolding AU - Salzberg, Steven AU - Sommer, Daniel AU - Puiu, Daniela AU - Lee, Vincent PY - 2008/09/26/ UR - http://dx.doi.org/10.1371/journal.pcbi.1000186 ER -