Frequently Asked Questions

How should I sequence the organism I’m interested in for optimal results in Simplicity™?

Well obviously every organism’s genome is different, so there isn’t a one size fits all. But for most bacterial genomes we have found that we can get a very high quality assembly with 1.5 to 2 million 150bp read pairs (paired end or mate pair). This should result in an assembly with between 75x to 125x coverage depending on the region of the genome.  
 
If you suspect that organism’s genome contains many repetitive regions, then longer reads (300bp paired end) would considerably improve the assembly.  

So for optimal results, we would recommend sequencing the genome you wish to analyse with Simplicity on a Illumina MiSeq, and take advantage of the 300bp reads. However as of January 2015, the Illumina HiSeq 2500 can now produce 250bp paired end reads in rapid mode while returning 10 times as many reads as a MiSeq run. While the HiSeq 3000 and 4000 can both produce 150bp paired end reads and return 100 times as many reads as a MiSeq! So if you’re
sequencing a lot of genomes the latter platforms will be much more cost effective. But ultimately, you should speak to your sequencing provider and see what they offer. 

How long will my analysis take in Simplicity™?

Not long! It will depend the size and composition of the genome, and exactly what types of analysis you want done. But including assembly and annotation, a bacterial genome would typically take 60 minutes from start to finish, with just a few clicks of the mouse. A viral genome would take less, usually around 20 minutes for everything. Don’t worry though, we’ll email you the
second your analysis is done with a full report. 

How do I upload my sequence data to Simplicity™?

Right now we have two options available; you can just upload it directly, or share it via DropBox. But we’re just finalising an app to directly share the data from Illumina BaseSpace to Simplicity™ meaning no downloading and uploading for you, you will be able to just log into BaseSpace and then into Simplicity™ and begin your analysis!