Find the information short reads miss

Short reads can struggle to characterize complex structural variants, resolve full-length RNA isoforms, and assess methylation in repetitive regions. This guide covers how PacBio HiFi long-read sequencing is used for each, with published examples, planning checklists, and links to relevant analysis tools.

Cover of the guide: Move beyond short reads

Inside the guide

Three applications and a plan for your first project

  • Structural variants

    Identify insertions, deletions, and complex rearrangements, including those in regions that are difficult to map with short reads.

  • Full-length isoforms

    Identify known and novel isoforms and alternative splicing with the Iso-Seq method, without reconstructing transcripts from short fragments.

  • Methylation from native DNA

    Detect CpG methylation directly from native DNA, including in difficult-to-map regions, and examine methylation alongside sequence variants and haplotypes.

  • Plan a HiFi study

    Review sample requirements, coverage, library preparation, and analysis considerations for the application you’re evaluating.

Is HiFi right for your study?

Find the application most relevant to your research question, then review the published evidence and planning considerations for that workflow.

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Illustration: short reads stop at a repeat region, while one HiFi read spans the repeat and the insertion inside itIllustration: short reads stop at a repeat region, while one HiFi read spans the repeat and the insertion inside it
Illustrative, not data. In repetitive regions short reads cannot map reliably. One HiFi read spans the repeat and the insertion inside it.

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