2SNV: Quasispecies Reconstruction from PacBio Reads

被引：0

作者：

Artyomenko, Alexander ^{[1
]}

Wu, Nicholas C. ^{[2
]}

Mangul, Serghei ^{[3
]}

Eskin, Eleazar ^{[3
]}

Sun, Ren ^{[4
]}

Zelikovsky, Alex ^{[1
]}

机构：

[1] Georgia State Univ, Dept Comp Sci, Atlanta, GA 30302 USA

[2] Scripps Res Inst, Dept Integrat Struct & Computat Biol, La Jolla, CA 92037 USA

[3] Univ Calif Los Angeles, Dept Comp Sci, Los Angeles, CA 90095 USA

[4] Univ Calif Los Angeles, Mol & Med Pharmacol, Los Angeles, CA 90095 USA

来源：

2015 IEEE 5TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES (ICCABS) | 2015年

关键词：

PacBio; viral quasispecies; SNV;

D O I：

暂无

中图分类号：

R318 [生物医学工程];

学科分类号：

0831 ;

摘要：

Pacific Biosciences (PacBio) sequencing is providing thousands of reads with the length up to 10,000 bases. In most cases this length is enough to cover entire region of interest however this technology has high (approximate to 15%) error rate. We propose a method for viral haplotype reconstruction using long SMRT reads. The proposed method based on correlation between SNVs and maximum likelihood for frequency estimation. When applied to PacBio reads from an Influenza A Virus (IAV) sample with ten variants, our method was able to reconstruct the nine most frequent.

引用

页数：1

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