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-now using cmake for Inchworm and Chrysalis builds
-new option '--include_supertranscripts' to output the supertranscripts in addition to the Trinity.fasta file.
-Updates for improved handling of non-strand-specific RNA-Seq and high polymorphism containing transcriptomes. (from v2.7.0-prerelease)
minor update... when running 'make' the installer now finds the chrysalis binaries in the right place. This is a cosmetic update. No change in function from v2.8.0
Updates for improved handling of non-strand-specific RNA-Seq and high polymorphism containing transcriptomes.
-minor updates to trinity gene splice modeler for python-3 compatibility
-update to R command execution that improves use on computing grids.
-incorporates salmon for quick expression estimates and filtering of likely artifacts
-drops bundling of jellyfish and samtools - now leverages user-installed versions of tools.
-overhauled supertranscript module, improvements around high-polymorphism situations.
-updated variant detection module, more flexible around STAR alignments and GATK usage
-misc bug fixes
(file: Trinity-v2.6.5.wExtSampleData.tar.gz includes additional sample data for testing Trinity protocol modules)
various bugfixes, revision of supertranscript module to improve compaction, expression-driven auto-filtering of likely artifacts
trinity 3rd party plugin components revised: jellyfish and samtools no longer bundled. Additional requirement of salmon.
Salmon v0.9.1 specifically required (or can run with --no_salmon to skip expression-based filtering)