Improving genome assemblies by sequencing PCR products with PacBio
Advances in sequencing technologies have dramatically reduced costs in producing high-quality draft genomes. However, there are still many contigs and possible misassembled regions in those draft genomes. Improving the quality of these genomes requires an efficient and economical means to close gaps...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2012-07-01
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| Series: | BioTechniques |
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| Online Access: | https://www.future-science.com/doi/10.2144/0000113891 |
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| author | Xiaojing Zhang Karen W. Davenport Wei Gu Hajnalka E. Daligault A. Christine Munk Hazuki Tashima Krista Reitenga Lance D. Green Cliff S. Han |
| author_facet | Xiaojing Zhang Karen W. Davenport Wei Gu Hajnalka E. Daligault A. Christine Munk Hazuki Tashima Krista Reitenga Lance D. Green Cliff S. Han |
| author_sort | Xiaojing Zhang |
| collection | DOAJ |
| description | Advances in sequencing technologies have dramatically reduced costs in producing high-quality draft genomes. However, there are still many contigs and possible misassembled regions in those draft genomes. Improving the quality of these genomes requires an efficient and economical means to close gaps and resequence some regions. Sequencing pooled gap region PCR products with Pacific Biosciences (PacBio) provides a significantly less expensive means for this need. We have developed a genome improvement pipeline with this strategy after decreasing a loading bias against larger PCR products in the PacBio process. Compared with Sanger technology, this approach is not only cost-effective but also can close gaps greater than 2.5 kb in a single round of reactions, and sequence through high GC regions as well as difficult secondary structures such as small hairpin loops. |
| format | Article |
| id | doaj-art-5d08a62df0bb4bcaab2054d7343cdd70 |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2012-07-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-5d08a62df0bb4bcaab2054d7343cdd702025-08-20T02:25:58ZengTaylor & Francis GroupBioTechniques0736-62051940-98182012-07-01531616210.2144/0000113891Improving genome assemblies by sequencing PCR products with PacBioXiaojing Zhang0Karen W. Davenport1Wei Gu2Hajnalka E. Daligault3A. Christine Munk4Hazuki Tashima5Krista Reitenga6Lance D. Green7Cliff S. Han81The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.A1The Genome Science Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, U.S.AAdvances in sequencing technologies have dramatically reduced costs in producing high-quality draft genomes. However, there are still many contigs and possible misassembled regions in those draft genomes. Improving the quality of these genomes requires an efficient and economical means to close gaps and resequence some regions. Sequencing pooled gap region PCR products with Pacific Biosciences (PacBio) provides a significantly less expensive means for this need. We have developed a genome improvement pipeline with this strategy after decreasing a loading bias against larger PCR products in the PacBio process. Compared with Sanger technology, this approach is not only cost-effective but also can close gaps greater than 2.5 kb in a single round of reactions, and sequence through high GC regions as well as difficult secondary structures such as small hairpin loops.https://www.future-science.com/doi/10.2144/0000113891Sequencinghairpin structureGC richPacBio |
| spellingShingle | Xiaojing Zhang Karen W. Davenport Wei Gu Hajnalka E. Daligault A. Christine Munk Hazuki Tashima Krista Reitenga Lance D. Green Cliff S. Han Improving genome assemblies by sequencing PCR products with PacBio BioTechniques Sequencing hairpin structure GC rich PacBio |
| title | Improving genome assemblies by sequencing PCR products with PacBio |
| title_full | Improving genome assemblies by sequencing PCR products with PacBio |
| title_fullStr | Improving genome assemblies by sequencing PCR products with PacBio |
| title_full_unstemmed | Improving genome assemblies by sequencing PCR products with PacBio |
| title_short | Improving genome assemblies by sequencing PCR products with PacBio |
| title_sort | improving genome assemblies by sequencing pcr products with pacbio |
| topic | Sequencing hairpin structure GC rich PacBio |
| url | https://www.future-science.com/doi/10.2144/0000113891 |
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