<it>De novo</it> assembly of highly diverse viral populations
<p>Abstract</p> <p>Background</p> <p>Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A <it>de novo</it> population consen...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2012-09-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/475 |
| _version_ | 1818049905675993088 |
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| author | Yang Xiao Charlebois Patrick Gnerre Sante Coole Matthew G Lennon Niall J Levin Joshua Z Qu James Ryan Elizabeth M Zody Michael C Henn Matthew R |
| author_facet | Yang Xiao Charlebois Patrick Gnerre Sante Coole Matthew G Lennon Niall J Levin Joshua Z Qu James Ryan Elizabeth M Zody Michael C Henn Matthew R |
| author_sort | Yang Xiao |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A <it>de novo</it> population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing <it>de novo</it> assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage.</p> <p>Results</p> <p>We present <it>VICUNA</it>, a <it>de novo</it> assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, <it>VICUNA</it> recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. <it>VICUNA</it> program is publicly available at: <url>http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software</url>.</p> <p>Conclusions</p> <p>We developed <it>VICUNA</it>, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While <it>VICUNA</it> was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.</p> |
| first_indexed | 2024-12-10T10:45:00Z |
| format | Article |
| id | doaj.art-0403d0e217dc4c69a42504e055c4ca55 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-10T10:45:00Z |
| publishDate | 2012-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-0403d0e217dc4c69a42504e055c4ca552022-12-22T01:52:11ZengBMCBMC Genomics1471-21642012-09-0113147510.1186/1471-2164-13-475<it>De novo</it> assembly of highly diverse viral populationsYang XiaoCharlebois PatrickGnerre SanteCoole Matthew GLennon Niall JLevin Joshua ZQu JamesRyan Elizabeth MZody Michael CHenn Matthew R<p>Abstract</p> <p>Background</p> <p>Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A <it>de novo</it> population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing <it>de novo</it> assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage.</p> <p>Results</p> <p>We present <it>VICUNA</it>, a <it>de novo</it> assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, <it>VICUNA</it> recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. <it>VICUNA</it> program is publicly available at: <url>http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software</url>.</p> <p>Conclusions</p> <p>We developed <it>VICUNA</it>, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While <it>VICUNA</it> was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.</p>http://www.biomedcentral.com/1471-2164/13/475 |
| spellingShingle | Yang Xiao Charlebois Patrick Gnerre Sante Coole Matthew G Lennon Niall J Levin Joshua Z Qu James Ryan Elizabeth M Zody Michael C Henn Matthew R <it>De novo</it> assembly of highly diverse viral populations BMC Genomics |
| title | <it>De novo</it> assembly of highly diverse viral populations |
| title_full | <it>De novo</it> assembly of highly diverse viral populations |
| title_fullStr | <it>De novo</it> assembly of highly diverse viral populations |
| title_full_unstemmed | <it>De novo</it> assembly of highly diverse viral populations |
| title_short | <it>De novo</it> assembly of highly diverse viral populations |
| title_sort | it de novo it assembly of highly diverse viral populations |
| url | http://www.biomedcentral.com/1471-2164/13/475 |
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