Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing
Long-read sequencing (LRS), like Oxford Nanopore Technologies, is usually associated with higher error rates compared to previous generations. Factors affecting the assembly quality are the integrity of DNA, the flowcell efficiency, and, not least all, the raw data processing. Among LRS-intended de...
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MDPI AG
2022-03-01
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| Online Access: | https://www.mdpi.com/2076-3417/12/6/3110 |
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| author | Antonella Schiavone Nicola Pugliese Rossella Samarelli Cosimo Cumbo Crescenzio Francesco Minervini Francesco Albano Antonio Camarda |
| author_facet | Antonella Schiavone Nicola Pugliese Rossella Samarelli Cosimo Cumbo Crescenzio Francesco Minervini Francesco Albano Antonio Camarda |
| author_sort | Antonella Schiavone |
| collection | DOAJ |
| description | Long-read sequencing (LRS), like Oxford Nanopore Technologies, is usually associated with higher error rates compared to previous generations. Factors affecting the assembly quality are the integrity of DNA, the flowcell efficiency, and, not least all, the raw data processing. Among LRS-intended de novo assemblers, Canu is highly flexible, with its dozens of adjustable parameters. Different Canu parameters were compared for assembling reads of <i>Salmonella</i><i>enterica</i> ser. Bovismorbificans (genome size of 4.8 Mbp) from three runs on MinION (N50 651, 805, and 5573). Two of them, with low quality and highly fragmented DNA, were not usable alone for assembly, while they were successfully assembled when combining the reads from all experiments. The best results were obtained by modifying Canu parameters related to the error correction, such as corErrorRate (exclusion of overlaps above a set error rate, set up at 0.40), corMhapSensitivity (the coarse sensitivity level, set to “high”), corMinCoverage (set to 0 to correct all reads, regardless the overlaps length), and corOutCoverage (corrects the longest reads up to the imposed coverage, set to 100). This setting produced two contigs corresponding to the complete sequences of the chromosome and a plasmid. The overall results highlight the importance of a tailored bioinformatic analysis. |
| first_indexed | 2024-03-09T20:08:21Z |
| format | Article |
| id | doaj.art-0620c29dfd4049bcac75a3f0f6bbed42 |
| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-03-09T20:08:21Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
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| series | Applied Sciences |
| spelling | doaj.art-0620c29dfd4049bcac75a3f0f6bbed422023-11-24T00:23:52ZengMDPI AGApplied Sciences2076-34172022-03-01126311010.3390/app12063110Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore SequencingAntonella Schiavone0Nicola Pugliese1Rossella Samarelli2Cosimo Cumbo3Crescenzio Francesco Minervini4Francesco Albano5Antonio Camarda6Department of Veterinary Medicine, University of Bari, 70010 Valenzano, ItalyDepartment of Veterinary Medicine, University of Bari, 70010 Valenzano, ItalyDepartment of Veterinary Medicine, University of Bari, 70010 Valenzano, ItalyHematology and Stem Cell Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, ItalyHematology and Stem Cell Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, ItalyHematology and Stem Cell Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, ItalyDepartment of Veterinary Medicine, University of Bari, 70010 Valenzano, ItalyLong-read sequencing (LRS), like Oxford Nanopore Technologies, is usually associated with higher error rates compared to previous generations. Factors affecting the assembly quality are the integrity of DNA, the flowcell efficiency, and, not least all, the raw data processing. Among LRS-intended de novo assemblers, Canu is highly flexible, with its dozens of adjustable parameters. Different Canu parameters were compared for assembling reads of <i>Salmonella</i><i>enterica</i> ser. Bovismorbificans (genome size of 4.8 Mbp) from three runs on MinION (N50 651, 805, and 5573). Two of them, with low quality and highly fragmented DNA, were not usable alone for assembly, while they were successfully assembled when combining the reads from all experiments. The best results were obtained by modifying Canu parameters related to the error correction, such as corErrorRate (exclusion of overlaps above a set error rate, set up at 0.40), corMhapSensitivity (the coarse sensitivity level, set to “high”), corMinCoverage (set to 0 to correct all reads, regardless the overlaps length), and corOutCoverage (corrects the longest reads up to the imposed coverage, set to 100). This setting produced two contigs corresponding to the complete sequences of the chromosome and a plasmid. The overall results highlight the importance of a tailored bioinformatic analysis.https://www.mdpi.com/2076-3417/12/6/3110flongleMinIONbacterial genome<i>Salmonella</i> <i>enterica</i>plasticityde novo assembly |
| spellingShingle | Antonella Schiavone Nicola Pugliese Rossella Samarelli Cosimo Cumbo Crescenzio Francesco Minervini Francesco Albano Antonio Camarda Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing Applied Sciences flongle MinION bacterial genome <i>Salmonella</i> <i>enterica</i> plasticity de novo assembly |
| title | Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing |
| title_full | Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing |
| title_fullStr | Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing |
| title_full_unstemmed | Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing |
| title_short | Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing |
| title_sort | factors affecting the quality of bacterial genomes assemblies by canu after nanopore sequencing |
| topic | flongle MinION bacterial genome <i>Salmonella</i> <i>enterica</i> plasticity de novo assembly |
| url | https://www.mdpi.com/2076-3417/12/6/3110 |
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