title: Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications.
abstract: BACKGROUND
  As the error rate is high and the distribution of errors across sites is non-uniform in next generation sequencing (NGS) data, it has been a challenge to estimate DNA polymorphism (θ) accurately from NGS data.
  
  
  RESULTS
  By computer simulations, we compare the two methods of data acquisition - sequencing each diploid individual separately and sequencing the pooled sample. Under the current NGS error rate, sequencing each individual separately offers little advantage unless the coverage per individual is high (>20X). We hence propose a new method for estimating θ from pooled samples that have been subjected to two separate rounds of DNA sequencing. Since errors from the two sequencing applications are usually non-overlapping, it is possible to separate low frequency polymorphisms from sequencing errors. Simulation results show that the dual applications method is reliable even when the error rate is high and θ is low.
  
  
  CONCLUSIONS
  In studies of natural populations where the sequencing coverage is usually modest (~2X per individual), the dual applications method on pooled samples should be a reasonable choice.
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, 135 Xingang West Road, Guangzhou 510275, China.
authors.forename: Ziwen
authors.initials: Z
authors.lastname: He
authors.forename: Xinnian
authors.initials: X
authors.lastname: Li
authors.forename: Shaoping
authors.initials: S
authors.lastname: Ling
authors.forename: Yun-Xin
authors.initials: YX
authors.lastname: Fu
authors.forename: Eric
authors.initials: E
authors.lastname: Hungate
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
mesh_terms: D032407:Avicennia / Q000378:metabolism; D018744:DNA, Plant / Q000235:genetics*; D004171:Diploidy; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015233:Models, Statistical; D011110:Polymorphism, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant
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