Summary of our poster at ONT London Calling 2017, by Catherine Zanchetta et al.
EVALUATION OF BASIC PARAMETERS
- For complex genome assembly, if a shearing and a size selection are performed on long fragments, very long reads can be obtained (40 kb shearing ? N50 = 24.6, up to 9 Gb).
- For small genomes, the quantity of data allows multiplexing which will reduce the cost of the sequencing.
- For diagnosis and production fields, the Rapid and the 1D protocols allow a fast library preparation (30 minutes – 3 hours).
- An important amount of DNA is required which is a technological limitation for some studies (minimum of 1.5 µg to produce 2Gb).
THE MINION FOR A BACTERIAL GENOME ASSEMBLY
- For small genomes, MinION combined to Illumina data generate high quality genome assemblies (0% of fragmented genes).
- Albacore 1.0.1. version reduces the error rate on Raw data (13.68%) but seems to create false homopolymers.
- The informatics pipeline from the sequencing to the assembly can be all completed in local (12 days duration).
- Important informatics resources are necessary, especially for the base calling (9.3 Gb run : 60 threads and 1.4 To workspace).