HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries.
Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) o...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284958/?tool=EBI |
| _version_ | 1818459276099715072 |
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| author | Sisi Zhou Yonggui Fu Jie Li Lingyu He Xingsheng Cai Qingyu Yan Xingqiang Rao Shengfeng Huang Guang Li Yiquan Wang Anlong Xu |
| author_facet | Sisi Zhou Yonggui Fu Jie Li Lingyu He Xingsheng Cai Qingyu Yan Xingqiang Rao Shengfeng Huang Guang Li Yiquan Wang Anlong Xu |
| author_sort | Sisi Zhou |
| collection | DOAJ |
| description | Second generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms. |
| first_indexed | 2024-12-14T23:11:47Z |
| format | Article |
| id | doaj.art-b243b5c2516a472f95aa4bb2adaf6ad7 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T23:11:47Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-b243b5c2516a472f95aa4bb2adaf6ad72022-12-21T22:44:11ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-01712e5225710.1371/journal.pone.0052257HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries.Sisi ZhouYonggui FuJie LiLingyu HeXingsheng CaiQingyu YanXingqiang RaoShengfeng HuangGuang LiYiquan WangAnlong XuSecond generation sequencing has been widely used to sequence whole genomes. Though various paired-end sequencing methods have been developed to construct the long scaffold from contigs derived from shotgun sequencing, the classical paired-end sequencing of the Bacteria Artificial Chromosome (BAC) or fosmid libraries by the Sanger method still plays an important role in genome assembly. However, sequencing libraries with the Sanger method is expensive and time-consuming. Here we report a new strategy to sequence the paired-ends of genomic libraries with parallel pyrosequencing, using a Chinese amphioxus (Branchiostoma belcheri) BAC library as an example. In total, approximately 12,670 non-redundant paired-end sequences were generated. Mapping them to the primary scaffolds of Chinese amphioxus, we obtained 413 ultra-scaffolds from 1,182 primary scaffolds, and the N50 scaffold length was increased approximately 55 kb, which is about a 10% improvement. We provide a universal and cost-effective method for sequencing the ultra-long paired-ends of genomic libraries. This method can be very easily implemented in other second generation sequencing platforms.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284958/?tool=EBI |
| spellingShingle | Sisi Zhou Yonggui Fu Jie Li Lingyu He Xingsheng Cai Qingyu Yan Xingqiang Rao Shengfeng Huang Guang Li Yiquan Wang Anlong Xu HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. PLoS ONE |
| title | HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. |
| title_full | HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. |
| title_fullStr | HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. |
| title_full_unstemmed | HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. |
| title_short | HTS-PEG: a method for high throughput sequencing of the paired-ends of genomic libraries. |
| title_sort | hts peg a method for high throughput sequencing of the paired ends of genomic libraries |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284958/?tool=EBI |
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