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Hicham Benzekri Paula Armesto Xavier Cousin Mireia Rovira Diego Crespo Manuel Alejandro Merlo David Mazurais Rocío Bautista Darío Guerrero-Fernández Noe Fernandez-Pozo Marian Ponce Carlos Infante Jose Luis Zambonino Sabine Nidelet Marta Gut Laureana Rebordinos Josep V Planas Marie-Laure Bégout M Gonzalo Claros Manuel Manchado 《BMC genomics》2014,15(1)
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Ting-Wen Chen Ruei-Chi Gan Yi-Feng Chang Wei-Chao Liao Timothy H. Wu Chi-Ching Lee Po-Jung Huang Cheng-Yang Lee Yi-Ywan M. Chen Cheng-Hsun Chiu Petrus Tang 《BMC genomics》2015,16(1)
Background
Whole genome sequence construction is becoming increasingly feasible because of advances in next generation sequencing (NGS), including increasing throughput and read length. By simply overlapping paired-end reads, we can obtain longer reads with higher accuracy, which can facilitate the assembly process. However, the influences of different library sizes and assembly methods on paired-end sequencing-based de novo assembly remain poorly understood.Results
We used 250 bp Illumina Miseq paired-end reads of different library sizes generated from genomic DNA from Escherichia coli DH1 and Streptococcus parasanguinis FW213 to compare the assembly results of different library sizes and assembly approaches. Our data indicate that overlapping paired-end reads can increase read accuracy but sometimes cause insertion or deletions. Regarding genome assembly, merged reads only outcompete original paired-end reads when coverage depth is low, and larger libraries tend to yield better assembly results. These results imply that distance information is the most critical factor during assembly. Our results also indicate that when depth is sufficiently high, assembly from subsets can sometimes produce better results.Conclusions
In summary, this study provides systematic evaluations of de novo assembly from paired end sequencing data. Among the assembly strategies, we find that overlapping paired-end reads is not always beneficial for bacteria genome assembly and should be avoided or used with caution especially for genomes containing high fraction of repetitive sequences. Because increasing numbers of projects aim at bacteria genome sequencing, our study provides valuable suggestions for the field of genomic sequence construction.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1859-8) contains supplementary material, which is available to authorized users. 相似文献12.
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