Fast-SG: an alignment-free algorithm for hybrid assembly. Issue 5 (5th May 2018)

• Record Type: Journal Article
• Authors: Di Genova, Alex; Ruz, Gonzalo A; Sagot, Marie-France; Maass, Alejandro
• Is Part Of: GigaScience. Volume 7:Issue 5(2018)
• Publication Date: 2018-05-05
• Subjects: hybrid assembly -- genome scaffolding -- alignment-free; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giy048
• Languages: English
• ISSNs: 2047-217X

Abstract

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 scaffoldinggraph 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.