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Author  |
Di Genova, A.; Ruz, G.A.; Sagot, M.F.; Maass, A. |
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Title |
Fast-SG: an alignment-free algorithm for hybrid assembly |
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Year |
2018 |
Publication |
Gigascience |
Abbreviated Journal |
GigaScience |
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Volume |
7 |
Issue |
5 |
Pages |
15 pp |
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Keywords |
hybrid assembly; genome scaffolding; alignment-free |
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Abstract |
Background: Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short-and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Results: Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffolding graph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Conclusions: Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost. |
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Address |
[Di Genova, Alex; Ruz, Gonzalo A.] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Santiago, Chile, Email: amaass@dim.uchile.cl |
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Publisher |
Oxford Univ Press |
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Language |
English |
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ISSN |
2047-217x |
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Notes |
WOS:000438568200001 |
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Call Number |
UAI @ eduardo.moreno @ |
Serial |
1036 |
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