I'm trying to resequence the genome of 30 strains of Bacillus Subtilis using good reference genomes (~4.2 MB size genome). We have extracted DNA from them and want to send them to an NGS service to have the samples library prepped, barcoded and sequenced. Afterwards we'd assemble the genomes back at our own lab.
Cost-wise and accuracy-wise for genome assembly, do you guys know if there's any significant difference between the Illumina platforms and Ion Torrent? It seems that a best bet would be to go with Miseq (2x150) or (2x250), but I'm not really familiar with Ion Torrent and was wondering if they were less expensive?
Have a good day, thanks all!