IDP

  • IDP is an gene Isoform Detection and Prediction tool
    from Second Generation Sequencing and PacBio sequencing.
    It offers very reliable gene isoform identification
    with high sensitivity
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Latest News: IDP 0.1.2 minor update is released ... read more

Getting Started

These simple steps will help you integrate IDP into your transcriptomics analysis pipeline.

Latest publication

Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Honoratus Van Bakel, Eric Schadt, Renee A. Reijo Pera, Jason Underwood, Wing Hung Wong
Characterization of the human ESC transcriptome by hybrid sequencing
Proc. Natl. Acad. Sci. USA 2013 110 (50) E4821-E4830 [preprint]

SpliceMap-LSC-IDP pipeline

This hESC transcriptome is identified by SpliceMap-LSC-IDP pipeline.

SpliceMap takes short reads from the Second Generation Sequencing platforms, such as Illumina, to detect exon junctions.

LSC makes use of the high-quality short reads to correct the long reads from PacBio platform. The output is the error-corrected long reads.

IDP uses the junction detections and the alignment of error-corrected long reads to detect the relatively short isoforms at full-length and predict the very long isoforms by statistical modeling.

    

Latest News

04-24-2014 - IDP 0.1.2 minor update is released

This minor update fixes several bugs.

04-17-2014 - IDP 0.1.1 minor update is released

This minor update fixes several bugs and is accompanied by a convenient, small-sized, test dataset available in the tutorial.

11-26-2013 - IDP 0.1 and the manual and a tutorial are released

IDP integrates short reads (e.g. Illumina data) and long reads (e.g. PacBio data) to identify gene isoforms (transcripts) from transcriptome (see Figure above).

11-26-2013: Hompage of hESC transcriptome identified by SpliceMap-LSC-IDP pipline is released.

The homepage of hESC transcriptome (H1 cell line) is released. You can also find novel genes, novel isoforms of existing genes (including pluripency markers) and novel ncRNA in this website:
http://www.healthcare.uiowa.edu/labs/au/IDP/hESC.asp

The details of this hESC transcriptome can be in our publication: Characterization of the human ESC transcriptome by hybrid sequencing [preprint]

11-26-2013: IDP and hESC transcriptome paper is released

Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Honoratus Van Bakel, Eric Schadt, Renee A. Reijo Pera, Jason Underwood, Wing Hung Wong
Characterization of the human ESC transcriptome by hybrid sequencing [preprint]
In press

For detailed information about this release, please see the release notes.