detonate/README at master · deweylab/detonate · GitHub

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        *** This file is autogenerated. Don't edit it directly. ***

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
   1. http://deweylab.biostat.wisc.edu/detonate/ref-eval.html
   2. http://genomebiology.com/2014/15/12/553
   3. http://deweylab.biostat.wisc.edu/detonate/detonate-1.11.tar.gz
   4. http://deweylab.biostat.wisc.edu/detonate/detonate-1.11-precompiled.tar.gz
   5. https://groups.google.com/d/forum/detonate-users
   6. http://deweylab.biostat.wisc.edu/detonate/vignette.html
   7. http://deweylab.biostat.wisc.edu/detonate/rsem-eval.html
   8. http://deweylab.biostat.wisc.edu/detonate/ref-eval.html
   9. http://deweylab.biostat.wisc.edu/detonate/ref-eval-estimate-true-assembly.html
  12. http://groups.google.com/group/detonate-users
  13. https://github.com/deweylab/detonate
  14. http://deweylab.biostat.wisc.edu/detonate/AxoJuveBlastema_RSEM-EVAL-1.4_Trinity.fasta.gz
  15. http://deweylab.biostat.wisc.edu/detonate/detonate-1.11.tar.gz
  16. http://deweylab.biostat.wisc.edu/detonate/detonate-1.10.tar.gz
  17. http://deweylab.biostat.wisc.edu/detonate/detonate-1.9.tar.gz
  18. http://deweylab.biostat.wisc.edu/detonate/detonate-1.8.1.tar.gz
  19. http://deweylab.biostat.wisc.edu/detonate/detonate-1.8.tar.gz
  20. http://deweylab.biostat.wisc.edu/detonate/detonate-20140123.tar.gz
  21. http://deweylab.biostat.wisc.edu/detonate/detonate-20140108.tar.gz