Uncovering the Meta-Transcriptome with Long-Read Sequencing - Shawn Levy, PhD

Shawn Levy, PhD - SVP of Applications & Scientific Affairs at Element Biosciences

  • Metatranscriptomics poses a challenge to short-read NGS
  • ORF prediction for LoopSeq+CappableSeq reads outperforms ORF prediction for uncorrected PacBio, ONT reads
  • LoopSeq+CappableSeq reduces erroneous mapping of transcripts to closely-related strains
  • Relative abundance of transcripts in mixture improved by LoopSeq+CappableSeq reads

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Transcript of Q&A Session

Q: Theoretically, once you make the library, whether you sequence with Illumina or AVITI, both are short-read technology and both should come out with similar quality, but you are pointing out that AVITI is better, why?

A: Importantly, the short-read sequencing which was done on Illumina was done short-read only. The Loop Seq was not applied to that short-read – a key differentiation. But to more appropriately answer your question, with the Loop Seq library, if we had sequenced that on AVITI and Illumina, the major conclusions would be the same. The differences would lie in some of the short-read performance differences – e.g. cost/Gb, relative base quality performance. It is really 2 different considerations.

Q: Have you tried the Loop technology on 10X Genomics cDNAs? Sometimes people use Nanopore to get full-length DNA of the single-cell libraries. Can you imagine whether we would be able to do this with Loop?

A: Conceivably it should be workable in a similar fashion, but it isn’t something we have experimentally looked at.

Q: Do you read the barcodes separately like Illumina or is it included or is it included in the 150 reads?

A: The UMI sequence is the initial part of R1. But then there are other indexes that can be used for sample and for plate. So you have multiple tiers of indexing capability. So the answer is both. It is captured in both cases.