Ion Torrent PGM 300bp Whole Gneome Shotgun Sequencing of E.coli Sakai
The Library of the EHEC Sakai strain were generated using 1 μg of the genomic DNA and the Ion Xpress Plus Fragment Library Kit comprising the Ion Shear chemistry according to the user guide. Libraries were barcoded with the Ion Xpress Barcode Adapters. For size selection E-Gel Size Select 2% Agarose Gels (Life Technologies) were used. All quality control analyses for the libraries were performed with a Caliper Labchip GX using the DNA High Sensitivity Assay (Caliper Life Sciences, Mainz, Germany). Library concentrations were determined with the Qubit dsDNA HS Assay Kit (Life Technologies). The barcoded library was diluted to 52 pM (2fold higher input than recommended), pooled equi-molar, and used with the Ion OneTouch 200 Template Kit v2 DL according to the User Guide for a 300bp run. A pooled sample was sequenced with the Ion PGM 300 Sequencing Kit on a 318 chip using 640 flows with TSS v3.0 software version with default settings, except that the more stringent filter was chosen and the Enable Base Recalibration option was turned off.