And it looks like a potentially cost-effective way to do DNA sequencing. At my lab, we are looking to DNA sequence and assemble the genomes (using genome assemblers like Velvet, SPAdes, etc) of 90 individual strains of Bacillus Subtilis. This is not De Novo assembly because we have many reference genomes available to resequence with.
Does anyone have any experience or thoughts about using MinION instead of an NGS (like Illumina Miseq or Hiseq) to obtain DNA sequences for the intended downstream application of assembling genomes? If it's really a poor man's NGS then it could help save us some money. Thanks!
I don't think it's a good idea for resequencing projects. Typically, resequencing is done for the purpose of finding novel SNPs between individual strains. The minION has a >10% error rate, making SNP identification and validation problematic. To me, the technology is meant for de novo assembly and is to be used in combination with other sequencing platforms, such as ion torrent or illumina.
In terms of error rate, it seems like software can correct to a certain degree, according to Supp Fig 2 from "A complete bacterial genome assembled de novo using only nanopore sequencing data", Nick Loman, 2015.
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Yes, it can get you a really good consensus. But if what you are sequencing is a heterogeneous population, it will be hard to tell real SNPs apart.
Well. You will find here many different answers and opinions
Mine is that MinION is still a promise. I am following and have set alerts that allow me to see how many papers are being published with this new technology. And it is far to be many...
I consider that MinION is still a promise if you pretend to use it as the only system for sequencing. Combined with Illumina data, however, it has been probed to be useful
It catched to my eyes the new Sequel from PacBio. They have increase 7X the output of the previous device. Output is now over many Gb of data, with a average sequence length of around 25Kb, and beyond (maximum is over 64Kb). With the new chip, costs have to be lower than before. It will allow you to unravel many different epigenetic modifications (read methylation) at the time of sequencing: a true value
It can depends on your way of being and thinking, but after many years waiting for the nanopore technology, I am founding myself a little bit sorry for not seeing what I was expecting
Sequel will be available in the second half of 2016 according to the press release. If you want to do something now, you have to use RS II. In addition, the typical pacbio read length is ~15kb after trimming. Only a small fraction of reads can reach 25kb. That being said, PacBio is arguably the best option so far to finish bacterial genomes.
I don't think it's a good idea for resequencing projects. Typically, resequencing is done for the purpose of finding novel SNPs between individual strains. The minION has a >10% error rate, making SNP identification and validation problematic. To me, the technology is meant for de novo assembly and is to be used in combination with other sequencing platforms, such as ion torrent or illumina.
In terms of error rate, it seems like software can correct to a certain degree, according to Supp Fig 2 from "A complete bacterial genome assembled de novo using only nanopore sequencing data", Nick Loman, 2015.
Yes, it can get you a really good consensus. But if what you are sequencing is a heterogeneous population, it will be hard to tell real SNPs apart.