Gene-boosted assembly of a novel bacterial genome from very short reads.
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 applie...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2008-09-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000186&type=printable |
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| author | Steven L Salzberg Daniel D Sommer Daniela Puiu Vincent T Lee |
| author_facet | Steven L Salzberg Daniel D Sommer Daniela Puiu Vincent T Lee |
| author_sort | Steven L Salzberg |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-baf95edd681c4a87a2bad973f80888db |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2008-09-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-baf95edd681c4a87a2bad973f80888db2025-08-20T02:17:29ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582008-09-0149e100018610.1371/journal.pcbi.1000186Gene-boosted assembly of a novel bacterial genome from very short reads.Steven L SalzbergDaniel D SommerDaniela PuiuVincent T LeeRecent 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.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000186&type=printable |
| spellingShingle | Steven L Salzberg Daniel D Sommer Daniela Puiu Vincent T Lee Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Computational Biology |
| title | Gene-boosted assembly of a novel bacterial genome from very short reads. |
| title_full | Gene-boosted assembly of a novel bacterial genome from very short reads. |
| title_fullStr | Gene-boosted assembly of a novel bacterial genome from very short reads. |
| title_full_unstemmed | Gene-boosted assembly of a novel bacterial genome from very short reads. |
| title_short | Gene-boosted assembly of a novel bacterial genome from very short reads. |
| title_sort | gene boosted assembly of a novel bacterial genome from very short reads |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000186&type=printable |
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