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!
The Ion torrent runs do tend to be less expensive. I don't think there is really a right or wrong answer here, and people certainly happily use both. I'll fully admit to some bias in that I much prefer Illumina data for a few reasons. Number 1 is that I am personally more familiar with it, having done far more work on the Illumina platform compared to Ion Torrent. Ion Torrent also has a higher error rate in terms of false indels than Illumina. For most applications it ends up not being a big issue though if your depth of sequencing is high enough.
You should be able to get quotes for both technologies from most providers, as most core facilities have both instruments on hand. Another point to keep in mind is the analysis portion. If you are doing it yourself, versus farming it out to a company or to a collaborator, that can effect your platform choice as well. For instance if a colleague is going to assemble the genomes and do all of the comparisons for you, it is usually worth going with their preferred platform. If you are doing it yourself and don't have much experience with either platform then that is a different story.