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.