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Last Updated: 10/15/2015
IMPORTANT: This GitHub repo/wiki will no longer be updated. All contents will remain frozen. All new Iso-Seq information, including SMRTLink 4.0 and above, tutorials, etc, will be now maintained at the new Iso-Seq "IsoSeq_SA3nUp" repository. Many of the links are now actually pointing to the new repo.
IMPORTANT NOTICE: The current version (2.2.3) of ToFU will NOT BE UPDATED. The next round of ToFu will be expected to be released after November 2015, after changes conforming to PacBio's new BAM format standard have been completed. All bugs and issues in ToFU 2.2.3 can be reported but will not be fixed until after the format changes.
Current ToFU version: v2.2.3 (see CHANGES)
The scripts in this repository are now compatible with SMRTAnalysis 2.3. It is a "beta" version of the RS_IsoSeq protocol that is supported in 2.3, 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.
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 wiki for more information.
Standard PacBio Open Source License that is associated with this package:
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