GeT | Implementation and evaluation of the MinIon (ONT London calling)
GeT : plateforme de Génomique et transcriptomique
ARN, Transcriptomique, RNA, Transcriptomics, ADN, génomique, DNA, genomics, cellule unique, single cell, Polymorphisme, polymorphism, NGS, Next Generation Sequencing , puces à ADN, microarrays, qPCR à Haut Débit (qPCR HD), High throughput Quantitative PCR, Analyses bioinformatiques et biostatistiques de données, Bioinformatics and biostatistical analysis
1487
post-template-default,single,single-post,postid-1487,single-format-standard,ajax_fade,page_not_loaded,smooth_scroll,,qode-theme-ver-3.8,wpb-js-composer js-comp-ver-5.4.5,vc_responsive
 

Actualités

Implementation and evaluation of the MinIon (ONT London calling)

  |   Site uniquement

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).

Poster présenté par Catherine Zanchetta