Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.
Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downs...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3726674?pdf=render |
| _version_ | 1819237799899955200 |
|---|---|
| author | Tsunglin Liu Cheng-Hung Tsai Wen-Bin Lee Jung-Hsien Chiang |
| author_facet | Tsunglin Liu Cheng-Hung Tsai Wen-Bin Lee Jung-Hsien Chiang |
| author_sort | Tsunglin Liu |
| collection | DOAJ |
| description | Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/. |
| first_indexed | 2024-12-23T13:26:05Z |
| format | Article |
| id | doaj.art-8792505374bc424bbe5f9dc46009e5ff |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-23T13:26:05Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-8792505374bc424bbe5f9dc46009e5ff2022-12-21T17:45:19ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6950310.1371/journal.pone.0069503Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.Tsunglin LiuCheng-Hung TsaiWen-Bin LeeJung-Hsien ChiangNext-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/.http://europepmc.org/articles/PMC3726674?pdf=render |
| spellingShingle | Tsunglin Liu Cheng-Hung Tsai Wen-Bin Lee Jung-Hsien Chiang Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. PLoS ONE |
| title | Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. |
| title_full | Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. |
| title_fullStr | Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. |
| title_full_unstemmed | Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. |
| title_short | Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. |
| title_sort | optimizing information in next generation sequencing ngs reads for improving de novo genome assembly |
| url | http://europepmc.org/articles/PMC3726674?pdf=render |
| work_keys_str_mv | AT tsunglinliu optimizinginformationinnextgenerationsequencingngsreadsforimprovingdenovogenomeassembly AT chenghungtsai optimizinginformationinnextgenerationsequencingngsreadsforimprovingdenovogenomeassembly AT wenbinlee optimizinginformationinnextgenerationsequencingngsreadsforimprovingdenovogenomeassembly AT junghsienchiang optimizinginformationinnextgenerationsequencingngsreadsforimprovingdenovogenomeassembly |