Linear time complexity de novo long read genome assembly with GoldRush
Abstract Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap – its most costly step – was improved in modern long read genome assemblers, these tools still often require excessive RAM when assembling a typical human da...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-38716-x |
| _version_ | 1797817945857982464 |
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| author | Johnathan Wong Lauren Coombe Vladimir Nikolić Emily Zhang Ka Ming Nip Puneet Sidhu René L. Warren Inanç Birol |
| author_facet | Johnathan Wong Lauren Coombe Vladimir Nikolić Emily Zhang Ka Ming Nip Puneet Sidhu René L. Warren Inanç Birol |
| author_sort | Johnathan Wong |
| collection | DOAJ |
| description | Abstract Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap – its most costly step – was improved in modern long read genome assemblers, these tools still often require excessive RAM when assembling a typical human dataset. Our work departs from this paradigm, foregoing all-vs-all sequence alignments in favor of a dynamic data structure implemented in GoldRush, a de novo long read genome assembly algorithm with linear time complexity. We tested GoldRush on Oxford Nanopore Technologies long sequencing read datasets with different base error profiles sourced from three human cell lines, rice, and tomato. Here, we show that GoldRush achieves assembly scaffold NGA50 lengths of 18.3-22.2, 0.3 and 2.6 Mbp, for the genomes of human, rice, and tomato, respectively, and assembles each genome within a day, using at most 54.5 GB of random-access memory, demonstrating the scalability of our genome assembly paradigm and its implementation. |
| first_indexed | 2024-03-13T09:00:51Z |
| format | Article |
| id | doaj.art-d6a30448c4c845bb9eefc3dcce11fd5d |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-13T09:00:51Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-d6a30448c4c845bb9eefc3dcce11fd5d2023-05-28T11:22:15ZengNature PortfolioNature Communications2041-17232023-05-011411910.1038/s41467-023-38716-xLinear time complexity de novo long read genome assembly with GoldRushJohnathan Wong0Lauren Coombe1Vladimir Nikolić2Emily Zhang3Ka Ming Nip4Puneet Sidhu5René L. Warren6Inanç Birol7Canada’s Michael Smith Genome Sciences Centre, BC CancerCanada’s Michael Smith Genome Sciences Centre, BC CancerCanada’s Michael Smith Genome Sciences Centre, BC CancerCanada’s Michael Smith Genome Sciences Centre, BC CancerCanada’s Michael Smith Genome Sciences Centre, BC CancerCanada’s Michael Smith Genome Sciences Centre, BC CancerCanada’s Michael Smith Genome Sciences Centre, BC CancerCanada’s Michael Smith Genome Sciences Centre, BC CancerAbstract Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap – its most costly step – was improved in modern long read genome assemblers, these tools still often require excessive RAM when assembling a typical human dataset. Our work departs from this paradigm, foregoing all-vs-all sequence alignments in favor of a dynamic data structure implemented in GoldRush, a de novo long read genome assembly algorithm with linear time complexity. We tested GoldRush on Oxford Nanopore Technologies long sequencing read datasets with different base error profiles sourced from three human cell lines, rice, and tomato. Here, we show that GoldRush achieves assembly scaffold NGA50 lengths of 18.3-22.2, 0.3 and 2.6 Mbp, for the genomes of human, rice, and tomato, respectively, and assembles each genome within a day, using at most 54.5 GB of random-access memory, demonstrating the scalability of our genome assembly paradigm and its implementation.https://doi.org/10.1038/s41467-023-38716-x |
| spellingShingle | Johnathan Wong Lauren Coombe Vladimir Nikolić Emily Zhang Ka Ming Nip Puneet Sidhu René L. Warren Inanç Birol Linear time complexity de novo long read genome assembly with GoldRush Nature Communications |
| title | Linear time complexity de novo long read genome assembly with GoldRush |
| title_full | Linear time complexity de novo long read genome assembly with GoldRush |
| title_fullStr | Linear time complexity de novo long read genome assembly with GoldRush |
| title_full_unstemmed | Linear time complexity de novo long read genome assembly with GoldRush |
| title_short | Linear time complexity de novo long read genome assembly with GoldRush |
| title_sort | linear time complexity de novo long read genome assembly with goldrush |
| url | https://doi.org/10.1038/s41467-023-38716-x |
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