DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
RSEM-EVAL is a reference-free evaluation method based on a novel probabilistic model that depends only on an assembly and the RNA-Seq reads used for its construction. Unlike N50, RSEM-EVAL combines multiple factors, including the compactness of an assembly and the support of the assembly from the RNA-Seq data, into a single, statistically-principled evaluation score. This score can be used to select a best assembler, optimize an assembler's parameters, and guide new assembler design as an objective function. In addition, for each contig within an assembly, RSEM-EVAL provides a score that assesses how well that contig is supported by the RNA-Seq data and can be used to filter unnecessary contigs.
REF-EVAL is a toolkit of reference-based measures, including contig, nucleotide, and pair precision, recall, and F1 scores, a novel kmer compression score, and several scores that compare induced kmer distributions between the assembly and the reference. REF-EVAL also includes a program to estimate the “true” assembly of a set of RNA-Seq reads, relative to a collection of full-length reference transcripts. See here, or ref-eval/README in the distribution, for detailed information.
DETONATE is motivated and described in detail in the following paper:
Bo Li*, Nathanael Fillmore*, Yongsheng Bai, Mike Collins, James A. Thomson, Ron Stewart, and Colin N. Dewey. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biology 2014, 15:553. link
* = equal contributions
The current version of DETONATE (1.11) is available here:
As a convenience, we also provide a precompiled version, for Linux. This precompiled version may or may not work for you; if it doesn't, please try to compile the version above, instead.
To build RSEM-EVAL and REF-EVAL, simply type “make” in the top-level detonate-1.11 directory, after you've upacked the tarball (tar xvf detonate-1.11.tar.gz). If you have trouble with any of this, please contact us.
A vignette with an extended example of the basic usage of DETONATE is available here, or in VIGNETTE in the distribution.
For information about using RSEM-EVAL, see here, or rsem-eval/README.md in the distribution.
For information about using REF-EVAL, see here, or ref-eval/README in the distribution.
For information about using REF-EVAL-ESTIMATE-TRUE-ASSEMBLY, see here, or ref-eval/README.REF-EVAL-ESTIMATE-TRUE-ASSEMBLY in the distribution.
RSEM-EVAL was coded by Bo Li, and REF-EVAL was coded by Nathanael Fillmore. Bo, Nate, and Colin Dewey jointly developed the RSEM-EVAL and REF-EVAL methodology, with feedback on the methodology from the other coauthors.
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A repository for the DETONATE source code is available at Github, here.
The RSEM-EVAL-guided Axolotl assembly described in the DETONATE paper (see above) is available here.
In DETONATE 1.11 (the current version), released on Jun 22, 2016, the following changes were made:
In DETONATE 1.10, released on Sep 1, 2015, the following changes were made:
In DETONATE 1.9, released on Mar 25, 2015, the following changes were made:
In DETONATE 1.8.1, released on Oct 2, 2014, the following changes were made:
In DETONATE 1.8, released on Sep 26, 2014, and comprised of RSEM-EVAL 1.8 and REF-EVAL 1.8, the following changes were made:
In DETONATE 20140123, comprised of RSEM-EVAL 1.6 and REF-EVAL 20140123, the following changes were made:
DETONATE 20140108, comprised of RSEM-EVAL 1.5 and REF-EVAL 20140108 was the initial release.