title: S. nepalensis isolate 6, MiSeq
design: Genome sequencing was carried out with a combination of Oxford Nanopore Sequencing and Illumina Miseq nano sequencing that produced 6.3 Gbases and 1.6 million (2x250) nucleotides with perfect Qscores. Briefly, genomic DNA from the bacterial strain (400 ng) was converted into a Nanopore library with the Rapid Barcoding library kit SQK-20 RAD004. The library was sequenced on a SpotON R9.4.1 FLO-MIN106 flowcell for 48h on a GridION sequencer. Basecalling was performed with Guppy 1.4.3, and demultiplexing was done with Porechops 0.2.3. The majority of the reads were 6 kb to 30 kb, although reads as long as 94 kb were also obtained. The Illumina Miseq sequencing was carried out by preparing shotgun genomic libraries with the Hyper Library construction kit from Kapa Biosystems (Roche). The library was quantitated by qPCR and sequenced on one MiSeq Nano flowcell for 251 cycles from each end of the fragments using a MiSeq 500-cycle sequencing kit version 2. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).