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DETONATE: DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

Overview

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 [1]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. [2]link

= equal contributions

Downloading

The current version of DETONATE (1.11) is available here:

 * [3]detonate-1.11.tar.gz

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.

 * [4]detonate-1.11-precompiled.tar.gz

Building/installation

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 [5]contact us.

Vignette

A vignette with an extended example of the basic usage of DETONATE is available [6]here, or in VIGNETTE in the distribution.

Usage

For information about using RSEM-EVAL, see [7]here, or rsem-eval/README.md in the distribution.

For information about using REF-EVAL, see [8]here, or ref-eval/README in the distribution.

For information about using REF-EVAL-ESTIMATE-TRUE-ASSEMBLY, see [9]here, or ref-eval/README.REF-EVAL-ESTIMATE-TRUE-ASSEMBLY in the distribution.

Authors

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.

Mailing list

Subscribe to DETONATE Users Email: [10]_____ [11][ Subscribe ] [12]Visit this group

Development

A repository for the DETONATE source code is available at Github, [13]here.

Axolotl assembly

The RSEM-EVAL-guided Axolotl assembly described in the DETONATE paper (see above) is available [14]here.

Changelog

In [15]DETONATE 1.11 (the current version), released on Jun 22, 2016, the following changes were made:

 * Reduced memory usage in RSEM-EVAL.
 * Changed build process to use the systemwide version of CMake,
   unless DETONATE is compiled with "NEED_CMAKE=yes make".
 * Restored missing "examples" directory in released version.

In [16]DETONATE 1.10, released on Sep 1, 2015, the following changes were made:

 * Added an option to store single-precision numbers in the hash
   table used for computing KC and kmer scores, so as to use less
   memory.

In [17]DETONATE 1.9, released on Mar 25, 2015, the following changes were made:

 * Canceled f function values from "Prior_score_on_contig_lengths"
   and "Correction_term".
 * Changed short to int to handle longer inferred insert sizes.

In [18]DETONATE 1.8.1, released on Oct 2, 2014, the following changes were made:

 * Updated the toy example to match that in the paper.

In [19]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:

 * Added support for paired-end data.
 * Improved the interface.

In [20]DETONATE 20140123, comprised of RSEM-EVAL 1.6 and REF-EVAL 20140123, the following changes were made:

 * Fixed UI bug in REF-EVAL related to --alignment-policy.
 * Incorporated changes from RSEM 1.2.9 into RSEM-EVAL.

[21]DETONATE 20140108, comprised of RSEM-EVAL 1.5 and REF-EVAL 20140108 was the initial release.

References

Visible links

deweylab / detonate

readme