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 0.1.6 major 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

08-04-2014 - Major Update to IDP

This is a major update to IDP and update includes changes to software requirements, additional features, and bug fixes.

08-01-2014 - Preparing long read outputs of LSC for use in IDP

Please concatenate the LSC outputs: corrected.fa with full.fa, and use this new fasta file as your long read inputs for IDP.

The reason is that corrected.fa will lose some flanking sequences on the long reads that were not corrected by short reads, and there still may be some informative junctions in that region. If we used only corrected.fa, we could lose this information. full.fa includes those flanking regions in addition to the corrections that were made. However, if we used only full.fa, it is likely the IDP algorithm could throw out many of those long reads for failing to find short read support for junctions in those regions. If you combine the two datasets, you will not suffer any loss of information, and any redundancies will be handled by IDP.

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.