DevNet | Contact Us | Terms of Use | Trademarks
Last Updated: 10/14/2014
The latest pbtranscript-tofu version: TBA. A new version of tofu that is compatible and improves upon the newly released SMRTAnalyss 2.3 will be released soon.
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.
Latest version of pbtranscript-tofu contains the following extensions:
- tofu_wrap.py is a wrapper around pbtranscript.py that automatically divides input into different size bins, runs clustering on the individual bins and combines them later, reducing unnecessary memory usage & runtime
- Support for "--fasta_fofn" input; also using multi-core for generating .bax.h5.fasta files for speedup
- Support for collapsing redundant transcripts based on alignment SAM file
- Minor changes to better support SMRTAnalysis 2.3 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:
#################################################################################$$
# Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted (subject to the limitations in the
# disclaimer below) provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
# GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
# BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
# USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
# SUCH DAMAGE.
#################################################################################$$