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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]
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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)
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