File: isoseq.md

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---
name: Iso-Seq
url: https://github.com/PacificBiosciences/IsoSeq
description: >
  Iso-Seq contains the newest tools to identify transcripts in PacBio single-molecule 
  sequencing data (HiFi reads).
---

Supports outputs generated by two commands:

- [IsoSeq `refine`](https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md#step-3---refine) trims poly(A) tails and removes concatemers.

- [IsoSeq `cluster`](https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md#step-4---clustering) performs clustering using hierarchical n\*log(n) alignment and iterative cluster merging.