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GRIT is genome-guided a transcript assembly tool designed and implemented by Nathan Boley, in collaboration with the Bickel and Celniker groups.
Apr 10, 2014
Released Version 1.1.2. This is includes all of the beta fixes, and updates the RAMPAGE class to properly handle auto read type identification.
Apr 1, 2014
Updated Version 1.1.2 beta to fix a couple of small bugs in the simulation code.
Mar 30, 2014
Updated the Version 1.1.2 beta to further reduce the memory footprint.
Mar 28, 2014
Version 1.1.2b (beta) has been updated, to fix a performance regression in 1.1.2a. The fix should also make estimating confidence bounds in very complex loci more efficient.
Mar 25, 2014
Version 1.1.2a (beta) has been released. Several people have reported frequent out of memory errors. This version should help to prevent most of these by writing teh design matrix files out to disk. In addition, two options have been added to config.py that allow the number of transcripts being built to be capped.
Mar 19, 2014
Version 1.1.1 has been released. This fixes several bugs introduced during the 1.1.0 refactor. I've also added a tar file containing a simple example run including a sample control file and the corresponding data.
Mar 17, 2014
Version 1.1.0 has been released. This is a significant refactor. In particular, GRIT is now distributed as a python module, which can be installed with easy_install, and the script has been renamed run_grit and moved into ./bin/. All config options have been moved to config.py, and code has been added to auto detect bam file types (if a reference annotation is provided).
Mar 12, 2014
The GRIT manuscript "Genome-guided transcript assembly by integrative analysis of RNA sequence data" and a companion paper "Diversity and dynamics of the Drosophila transcriptome" which made heavy use GRIT, will be published online Sunday, March 17. I'll post a link when they are online.
Feb 13, 2014
Version 1.0.0 has been released. This is the version (plus some relatively minor bug fixes) that was used for the Nature Biotech Paper.
Feb 11, 2014
The method manuscript "Genome-guided transcript assembly from integrative analysis of RNA sequence data" has been accepted for publication at Nature Biotechnology.
Jan 24, 2014
A browser track comparing annotations prepared by GRIT, Cufflinks, Trinity+Rsem, and Scripture in 20 day old fly heads are available.
April 10, 2013
We will present a poster "The modENCODE Drosophila Transcriptome Annotation Project reveals the necessity of integrated analysis for transcript assembly" at The Biology of Genomes.