Real-time resolution of short-read assembly graph using ONT long reads.
A streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequencing resources and reducing time-to-result. A previous approach implemented in npScarf provided an efficient streaming algorithm for hybrid assembly but was relatively pro...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2021-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1008586 |
| _version_ | 1819007701033680896 |
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| author | Son Hoang Nguyen Minh Duc Cao Lachlan J M Coin |
| author_facet | Son Hoang Nguyen Minh Duc Cao Lachlan J M Coin |
| author_sort | Son Hoang Nguyen |
| collection | DOAJ |
| description | A streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequencing resources and reducing time-to-result. A previous approach implemented in npScarf provided an efficient streaming algorithm for hybrid assembly but was relatively prone to mis-assemblies compared to other graph-based methods. Here we present npGraph, a streaming hybrid assembly tool using the assembly graph instead of the separated pre-assembly contigs. It is able to produce more complete genome assembly by resolving the path finding problem on the assembly graph using long reads as the traversing guide. Application to synthetic and real data from bacterial isolate genomes show improved accuracy while still maintaining a low computational cost. npGraph also provides a graphical user interface (GUI) which provides a real-time visualisation of the progress of assembly. The tool and source code is available at https://github.com/hsnguyen/assembly. |
| first_indexed | 2024-12-21T00:28:45Z |
| format | Article |
| id | doaj.art-0ca21fd85389402bae7ad58a11bf3f13 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-21T00:28:45Z |
| publishDate | 2021-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-0ca21fd85389402bae7ad58a11bf3f132022-12-21T19:21:55ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582021-01-01171e100858610.1371/journal.pcbi.1008586Real-time resolution of short-read assembly graph using ONT long reads.Son Hoang NguyenMinh Duc CaoLachlan J M CoinA streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequencing resources and reducing time-to-result. A previous approach implemented in npScarf provided an efficient streaming algorithm for hybrid assembly but was relatively prone to mis-assemblies compared to other graph-based methods. Here we present npGraph, a streaming hybrid assembly tool using the assembly graph instead of the separated pre-assembly contigs. It is able to produce more complete genome assembly by resolving the path finding problem on the assembly graph using long reads as the traversing guide. Application to synthetic and real data from bacterial isolate genomes show improved accuracy while still maintaining a low computational cost. npGraph also provides a graphical user interface (GUI) which provides a real-time visualisation of the progress of assembly. The tool and source code is available at https://github.com/hsnguyen/assembly.https://doi.org/10.1371/journal.pcbi.1008586 |
| spellingShingle | Son Hoang Nguyen Minh Duc Cao Lachlan J M Coin Real-time resolution of short-read assembly graph using ONT long reads. PLoS Computational Biology |
| title | Real-time resolution of short-read assembly graph using ONT long reads. |
| title_full | Real-time resolution of short-read assembly graph using ONT long reads. |
| title_fullStr | Real-time resolution of short-read assembly graph using ONT long reads. |
| title_full_unstemmed | Real-time resolution of short-read assembly graph using ONT long reads. |
| title_short | Real-time resolution of short-read assembly graph using ONT long reads. |
| title_sort | real time resolution of short read assembly graph using ont long reads |
| url | https://doi.org/10.1371/journal.pcbi.1008586 |
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