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@article{Wymant:2018:ve/vey007,
author = {Wymant, C and Blanquart, F and Golubchik, T and Gall, A and Bakker, M and Bezemer, D and Croucher, NJ and Hall, M and Hillebregt, M and Ong, SH and Ratmann, O and Albert, J and Bannert, N and Fellay, J and Fransen, K and Gourlay, A and Grabowski, MK and Gunsenheimer-Bartmeyer, B and Günthard, HF and Kivelä, P and Kouyos, R and Laeyendecker, O and Liitsola, K and Meyer, L and Porter, K and Ristola, M and van, Sighem A and Berkhout, B and Cornelissen, M and Kellam, P and Reiss, P and Fraser, C and BEEHIVE, Collaboration},
doi = {ve/vey007},
journal = {Virus Evolution},
title = {Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver},
url = {http://dx.doi.org/10.1093/ve/vey007},
volume = {4},
year = {2018}
}

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TY  - JOUR
AB  - Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied sh
AU  - Wymant,C
AU  - Blanquart,F
AU  - Golubchik,T
AU  - Gall,A
AU  - Bakker,M
AU  - Bezemer,D
AU  - Croucher,NJ
AU  - Hall,M
AU  - Hillebregt,M
AU  - Ong,SH
AU  - Ratmann,O
AU  - Albert,J
AU  - Bannert,N
AU  - Fellay,J
AU  - Fransen,K
AU  - Gourlay,A
AU  - Grabowski,MK
AU  - Gunsenheimer-Bartmeyer,B
AU  - Günthard,HF
AU  - Kivelä,P
AU  - Kouyos,R
AU  - Laeyendecker,O
AU  - Liitsola,K
AU  - Meyer,L
AU  - Porter,K
AU  - Ristola,M
AU  - van,Sighem A
AU  - Berkhout,B
AU  - Cornelissen,M
AU  - Kellam,P
AU  - Reiss,P
AU  - Fraser,C
AU  - BEEHIVE,Collaboration
DO  - ve/vey007
PY  - 2018///
SN  - 2057-1577
TI  - Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver
T2  - Virus Evolution
UR  - http://dx.doi.org/10.1093/ve/vey007
UR  - https://www.ncbi.nlm.nih.gov/pubmed/29876136
UR  - http://hdl.handle.net/10044/1/60768
VL  - 4
ER  -

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