Please use this identifier to cite or link to this item:
Title: BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads
Authors: Hong, L.Z.
Hong, S.
Wong, H.T.
Aw, P.P.
Cheng, Y.
Wilm, A.
de Sessions, P.F.
Lim, S.G. 
Nagarajan, N. 
Hibberd, M.L. 
Quake, S.R.
Burkholder, W.F.
Keywords: algorithm
computer program
DNA sequence
genetic variability
hepatitis B
Hepatitis B virus
high throughput sequencing
Genetic Variation
Hepatitis B
Hepatitis B virus
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Issue Date: 2014
Citation: Hong, L.Z., Hong, S., Wong, H.T., Aw, P.P., Cheng, Y., Wilm, A., de Sessions, P.F., Lim, S.G., Nagarajan, N., Hibberd, M.L., Quake, S.R., Burkholder, W.F. (2014). BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome biology 15 (11) : 517. ScholarBank@NUS Repository.
Rights: Attribution 4.0 International
Abstract: We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.
Source Title: Genome biology
ISSN: 1474760X
DOI: 10.1186/s13059-014-0517-9
Rights: Attribution 4.0 International
Appears in Collections:Elements
Staff Publications

Show full item record
Files in This Item:
File Description SizeFormatAccess SettingsVersion 
10_1186_s13059-014-0517-9.pdf657.6 kBAdobe PDF



Google ScholarTM



This item is licensed under a Creative Commons License Creative Commons