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Last Updated: 05/12/2014
The latest pbtranscript-tofu version: 0.2.tofu.134691
The scripts in this repository are now compatible with SMRTAnalysis 2.2. It is a "beta" version of the RS_IsoSeq protocol that is supported in 2.2, meaning that it extends the existing RS_IsoSeq code base, and is an unofficial, developemental version of RS_IsoSeq. This beta version is only accessible via command line. The command line name of the official RS_IsoSeq is pbtranscript, to differentiate from the official version, in the tutorials we will refer to the beta version provided on this site as pbtranscript-tofu.
Functionalities provided in pbtranscript-tofu are highly developmental and may not make it into the next version of official RS_IsoSeq.
Latest version of pbtranscript-tofu contains the following extensions:
- Support for identifying full-length transcripts that does not have polyA tail (ex: RT-PCR transcripts)
- Support for collapsing redundant transcripts based on alignment SAM file
- Faster I/O for base QV reading in clustering, resulting in overall speedup
- Minor changes to better support SMRTAnalysis 2.2 framework
The scripts in this repository is developed for the purpose of analyzing transcriptome data generated using the PacBio(R) Iso-Seq(TM) protocol.
This code is not part of the official PacBio software package and is developed solely by Elizabeth Tseng. The official software version is the RS_IsoSeq protocol. Use this code at your own risk.
The Iso-Seq (Isoform Sequencing) protocol refers to PacBio’s proprietary methods and applications for transcriptome sequencing. Please refer to the resources below, as well as the wiki for more information:
- Iso-Seq Webinar (recorded 1/22/2014)
- Iso-Seq Webinar Slides
- Iso-Seq Webinar Q&A
Standard PacBio Open Source License that is associated with this package:
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