This post is a condensed version of a discussion we had in my office after PacBio announced their new Sequel long-read sequencer. This contains some hand-wavy statements and calculations, however the aim is to provide some insight into how we make decisions about sequencing here at the JGI. I wrote this blog post jointly with Alex Copeland the QC and Assembly group lead, and Alicia Clum the Genome Assembly and Analysis lead. Alicia recently joined twitter and you should definitely follow her. She may have mentioned that she wanted everyone to send her all their genome assembly questions but I could have misheard her.
The PacBio Sequel specifications indicate ~7x the output per SMRT cell at half the instrument price of the RSII ($300k vs. $750k). The caveat being that the individual SMRT cell price will be 2-3X more expensive. Keith Bradnam has a round up of all the news and blogs discussing the announcement. The Joint Genome Institute (JGI) will be receiving one of the Sequels in November as part of the early access program. Therefore we are already in the process of considering how to integrate the Sequel into our existing pipelines.
The JGI offers several assembly products for Prokaryotes and Eukaryotes. Each product is a combination of different DNA extraction, library preparation, sequencing and informatics post-processing. Our microbial isolate products relevant to the PacBio announcement and this discussion are:
Prokaryotic Minimal Draft - A cultured Bacteria or Archaea, with a typically simple genome. Sequenced as a 2x150bp, 275bp insert fragment library on an Illumina 1T HiSeq with 48x pooling. We sequenced 1050 of these last fiscal year.
Prokaryotic Improved Draft - Library preparation using AMPure bead purification to select fragments greater than 10kbp. Sequenced on the PacBio RSII usually requiring only a single SMRT cell. A "better" product than the prokaryotic minimal draft because this often produces a single contig assembly, this is used for more complex prokaryotic genomes such as Actinomycetes. We sequenced 250 of these last fiscal year, and expect to produce ~500 this year.
Eukaryotic Minimal Draft - A cultured eukaryote, usually fungal. Similar to the prokaryotic minimal draft this is sequenced as a 2x150bp, 275bp insert fragment library on an Illumina 1T HiSeq with 8x pooling. Typically we sequence eukaryotes with more tractable genomes, such as Aspergillus, using this protocol. We sequenced 100 of these in the last fiscal year.
Eukaryotic Standard Draft - Two libraries generated and sequenced using the ALLPATHS-LG recipe: one standard Illumina fragment, and one 4kb long mate pair library. The long mate pairs using ALLPATHS-LG allow us to generate a better assembly than the minimal draft. We sequenced ~100 of these in the last fiscal year.
Eukaryotic Improved Draft - Same as a prokaryotic improved draft except that this is larger eukaryotic genome and requires ~5 SMRT cells for a ~40Mbp haploid genome. Extra attention is required in assembly due to the presence of organelles. We sequenced less than 10 of these in the last fiscal year. For the last few years this product has been a combined draft of one Illumina fragment library, one Illumina long mate pair library and one PacBio library. This fiscal year we will now switch to a 20kbp Blue Pippin library which has higher labour and reagent costs, compared with an AMPure PacBio library, but which produces a better assembly.
You may notice that there is no 'Prokaryotic Standard Draft' in this list, i.e. no combined standard fragment and long mate pair sequencing of Prokaryotes. The reason is that producing the long mate pair library and sequencing on Illumina costs us about the same as sequencing on the PacBio RSII, while a PacBio 10kbp library produces a better assembly overall with the same current throughput.
For the same reason this fiscal year we are also discontinuing the Illumina "Eukaryotic Standard Draft". Recent analysis by Alicia shows that we can also get better assemblies switching to 10kbp+ PacBio libraries for eukaryotes rather than continuing with the long mate pair and fragment approach. The extra costs associated with preparing two different libraries versus a single PacBio library which also produces a more contiguous assembly means we will do half our fungal draft sequencing on the PacBio for the next fiscal year.
This then leads into the Sequel announcement - given that we already use ~5 SMRT cells for a eukaryotic genome, switching to the PacBio Sequel will likely mean that this product type will become even more cost effective. This is calculated using the announced numbers: ~7X the GBp per SMRT cell at 2-3X the SMRT cell cost would mean approximately ~2X cost saving.
The second point, and the reason to write this blog post, is what effect could the PacBio Sequel have on our current prokaryotic sequencing? Considering our existing PacBio prokaryotic sequencing, switching to the Sequel would mean more data that we do not necessarily require because, in most cases, one SMRT cell is sufficient to get a complete assembly for the average Bacteria/Archaea. Using one Sequel SMRT cell would make each prokaryotic assembly 2-3X more expensive than it already is. Therefore, it is unlikely we would do a straight switch over to the Sequel for Prokaryotes if cost were the only consideration. There are however two caveats to this.
The first caveat is that we are currently in the middle of sequencing 1000 Actinomycetes - bacteria that we sequence on the PacBio RSII as prokaryotic improved drafts. These are high GC, repeat-rich genomes, with especially long repeats, meaning 2-3 RSII SMRT cells are usually needed to produce sufficient numbers of reads long enough to span repeats. Therefore in the cases where we are already using multiple SMRT cells, switching to the Sequel would make sense for the same cost-saving described above. An added advantage, and worth mentioning in this context, is that PacBio sequencing displays no GC-bias, so this is an additional advantage for organisms with very high or low GC genomes. An example is the JGI recently completed sequencing and assembly of a Piromyces fungal genome with <20% GC which, for the last decade, has resisted all previous attempts at sequencing and assembly.
The second caveat is that the increased Sequel capacity makes pooling important. If you are unfamiliar with pooling, this is the process of combining multiple different DNA libraries together and then sequencing them all together, usually in an Illumina flowcell. A unique oligonucleotide 'barcode' is added to each library during preparation which allows the FASTQ data to be separated back into the original library after sequencing. If we could take advantage of the extra Sequel capacity and sequence 7 microbes per SMRT cell using barcodes, then the same cost savings would apply.
An additional possibility that would streamline laboratory preparation, and therefore cost, is to skip barcoding entirely. The reason being that the long-read overlaps are unambiguous enough that the genomes would simply assemble together out of the pool, similar to that of a metagenome. This would however require the production planning to ensure that the pairwise genome distance between any two organisms is large enough to ensure no cross-assembly. I had a short twitter conversation and this approach with Mick Watson who outlined some possible problems.
Why don't we sequence everything on PacBio?
In the process of discussing the Sequel the question arose that we have considered multiple times in the past: why don't we sequence all microbes on the PacBio? One reason is that an Illumina prokaryotic minimal draft costs around 1/10th as much as a PacBio prokaryotic improved draft. Sequencing 1000 microbes on Illumina instead of PacBio RSII is the difference in approximately $360,000 a year.
This is a pure cost-only comparison and if cost was the only factor, then we would sequence everything on Illumina 1T using a standard fragment library. However, assembly quality is extremely important, and is why we don't only do this. If the costs drop in future with the new PacBio Sequel platform, we will reevaluate opportunities for applying PacBio to prokaryotic isolate sequencing.