dc.contributor.author | Grytten, Ivar | |
dc.contributor.author | Rand, Knut D | |
dc.contributor.author | Nederbragt, Alexander J | |
dc.contributor.author | Sandve, Geir K | |
dc.date.accessioned | 2020-04-07T05:03:08Z | |
dc.date.available | 2020-04-07T05:03:08Z | |
dc.date.issued | 2020 | |
dc.identifier.citation | BMC Genomics. 2020 Apr 06;21(1):282 | |
dc.identifier.uri | http://hdl.handle.net/10852/74399 | |
dc.description.abstract | Background
Graph-based reference genomes have become popular as they allow read mapping and follow-up analyses in settings where the exact haplotypes underlying a high-throughput sequencing experiment are not precisely known. Two recent papers show that mapping to graph-based reference genomes can improve accuracy as compared to methods using linear references. Both of these methods index the sequences for most paths up to a certain length in the graph in order to enable direct mapping of reads containing common variants. However, the combinatorial explosion of possible paths through nearby variants also leads to a huge search space and an increased chance of false positive alignments to highly variable regions.
Results
We here assess three prominent graph-based read mappers against a hybrid baseline approach that combines an initial path determination with a tuned linear read mapping method. We show, using a previously proposed benchmark, that this simple approach is able to improve overall accuracy of read-mapping to graph-based reference genomes.
Conclusions
Our method is implemented in a tool Two-step Graph Mapper, which is available at https://github.com/uio-bmi/two_step_graph_mapperalong with data and scripts for reproducing the experiments. Our method highlights characteristics of the current generation of graph-based read mappers and shows potential for improvement for future graph-based read mappers. | |
dc.language.iso | eng | |
dc.rights | The Author(s) | |
dc.rights | Attribution 4.0 International | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.title | Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods | |
dc.type | Journal article | |
dc.date.updated | 2020-04-07T05:03:10Z | |
dc.creator.author | Grytten, Ivar | |
dc.creator.author | Rand, Knut D | |
dc.creator.author | Nederbragt, Alexander J | |
dc.creator.author | Sandve, Geir K | |
dc.identifier.cristin | 1856152 | |
dc.identifier.doi | https://doi.org/10.1186/s12864-020-6685-y | |
dc.identifier.urn | URN:NBN:no-77512 | |
dc.type.document | Tidsskriftartikkel | |
dc.type.peerreviewed | Peer reviewed | |
dc.identifier.fulltext | Fulltext https://www.duo.uio.no/bitstream/handle/10852/74399/1/12864_2020_Article_6685.pdf | |
dc.type.version | PublishedVersion | |
cristin.articleid | 282 | |