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Division of Infectious Diseases
University of Geneva Hospitals
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Edena v3: de novo short reads assembler

References

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J.
Genome Research. 18:802-809, 2008.

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.
Hernandez D, Tewhey R, Veyrieras JB, Farinelli L, Osterċs M, François P, Schrenzel J.
Bioinformatics. 2013 Oct 15. [Epub ahead of print]

Announcement list

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Contact

Dr David HERNANDEZ

Download

Edena V3.131028 (October 28, 2013)

  • Minor bugs fix
  • Some speed optimizations
  • Better errors checking
  • Edena V3.130110 (January 11, 2013)

  • Updated the interactive shell. Now available is a command that greatly helps in producing primers to check targeted regions in an assembly
  • Updated the "rapid files examination" procedure to make it more robust. Previous version could underestimate the number of reads, which caused a program interruption
  • EdenaV3.121122 (November 27, 2012)

  • Edena is now open source under the General Public Licence V3
  • Interactive shell: This is a simple shell that was initially implemented for development purposes. It allows querying the overlaps string graph at targeted nodes. It provides information on the graph topology, nodes coverage, paired-end mapping as well as the possibility to extract DNA sequences. It is a powerful tool to check and/or manually resolve targeted parts of an assembly. This functionality is currently provided "as is" since it is not thoroughly documented. More is to come about this.
  • version 3 dev 120926 (September 26, 2012)

  • New license: Edena can now be freely used by anyone as long as it is quoted.
  • Improved the assembly reliability
  • Bug fixes
  • Edena3dev120926 for Linux-64

    version 3 dev 120626 (June 26, 2012)

  • Bug fixes
  • Edena3dev120626 for Linux-64
    Edena3dev120626 for Linux-32

    version 3 dev 120615 (June 22, 2012)

  • Added support for long paired-ends (Illumina mate-pairs) reads dataset
  • Multi-threading for the overlapper
  • Bug fixes
  • Edena3dev120615 for Linux-64
    Edena3dev120615 for Linux-32

    version 3 dev 110920 (September 20, 2011)

  • Improved the reliability of the paired-end algorithm
  • Edena3dev110920 for Linux-64
    Edena3dev110920 for Linux-32

    version 3 dev 110815 (August 15, 2011)

  • Fixed a bug that caused only half of the paired-end information to be considered
  • Edena3dev110815 for Linux-64
    Edena3dev110815 for Linux-32

    version 3 dev 110814 (August 14, 2011)

  • Added support for multiple paired-end dataset issued from different insert-size preparations
  • "Floating point exception" bug fixed
  • Edena3dev110814 for Linux-64
    Edena3dev110814 for Linux-32

    version 3 dev 110705 (July 2011)

    Edena3dev110705 for Linux-64
    Edena3dev110705 for Linux-32

    version 2.1.1 (2008)

  • Obsolete
  • Edena 2.1.1 for Linux-32
    Edena 2.1.1 for Linux-64
    Edena 2.1.1 for Windows (experimental)

    Staphylococcus aureus strain MW2 reads dataset (this dataset is the one used in the 2008 publication):

    mw2Reads.seq.gz (63Mo)

       
         
               

    Revised Oct 28, 2013 - © 2003-2014 Genomic Research Laboratory, Geneva