MetaCarvel: linking assembly graph motifs to biological variants
| dc.citation.articleNumber | 174 | |
| dc.citation.journalTitle | Genome Biology | |
| dc.citation.volumeNumber | 20 | |
| dc.contributor.author | Ghurye, Jay | |
| dc.contributor.author | Treangen, Todd | |
| dc.contributor.author | Fedarko, Marcus | |
| dc.contributor.author | Hervey, W. Judson | |
| dc.contributor.author | Pop, Mihai | |
| dc.date.accessioned | 2019-11-14T17:52:27Z | |
| dc.date.available | 2019-11-14T17:52:27Z | |
| dc.date.issued | 2019 | |
| dc.description.abstract | Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains. Previous methods have addressed these issues by smoothing genomic variants. We present a variant-aware metagenomic scaffolder called MetaCarvel, which combines new strategies for repeat detection with graph analytics for the discovery of variants. We show that MetaCarvel can accurately reconstruct genomic segments from complex microbial mixtures and correctly identify and characterize several classes of common genomic variants. | |
| dc.identifier.citation | Ghurye, Jay, Treangen, Todd, Fedarko, Marcus, et al.. "MetaCarvel: linking assembly graph motifs to biological variants." <i>Genome Biology,</i> 20, (2019) Biomed Central: https://doi.org/10.1186/s13059-019-1791-3. | |
| dc.identifier.digital | s13059-019-1791-3 | |
| dc.identifier.doi | https://doi.org/10.1186/s13059-019-1791-3 | |
| dc.identifier.uri | https://hdl.handle.net/1911/107688 | |
| dc.language.iso | eng | |
| dc.publisher | Biomed Central | |
| dc.rights | This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/), | |
| dc.title | MetaCarvel: linking assembly graph motifs to biological variants | |
| dc.type | Journal article | |
| dc.type.dcmi | Text | |
| dc.type.publication | publisher version |
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