Should I use Illumina or Ion Torrent for producing data intended for genome resequencing/assembly?

Question

[jerrybug109]

Hi all,

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!

[User 59]

Not considering PacBio? Far more chance of delivering yourself an assembly in as few contigs as possible..

And crossposted to SeqAnswers: http://seqanswers.com/forums/showthread.php?t=63508

[Adrian Pelin]

Since this is resequencing and implied variant discovery... I would not personally recommend PacBio.

[User 59]

Then why is the question about assembly?

[stolarek.ir]

I wouldn't worry that much about costs nowadays. You can always ship for sequencing to Korea. It's actually a very good choice if you have a lot to sequence. If get to high amount of coverage (which for variant discovery will probably be this 100X or whatever) I don't think that Ion vs Illumina will matter that much, as they are comparable for resequencing projects. However for the assembly, it might be worthwile looking at results from something like PacBio (which actually is made for microbial assembly nowadays), and decide, if this type of data balances higher costs. You can also do something non specific with Illumina (I think you can easilly get 1000 bp biological reads, but you won't find kits for this).

Answer 1

[DG]

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.

[Adrian Pelin]

I am currently starting to get familiar with Ion Torrent, having an Illumina background. I have handled a bit of their sample data, and with the latest chemistry I must say it's impressive and competitive. Although officially Ion Torrent error rates can go up to 2x compared to Illumina, it depends on the sequencing provider and the library prep, I have seen some Illumina libraries with 454-like quality... I am scheduled to complete a few sequencing runs with Ion Torrent and will be happy to report back on how I find my own data.