Ray 1.4.0: built-in scaffolder & more
Dear Ray users,
Ray 1.4.0 is now available.
The most significant change is the built-in scaffolder.
The second most significant change is the new algorithm that finds
assembly seeds.
Also, I added a lot of output files in Ray.
They are listed here:
Finally, our new website http://denovoassembler.sf.net is hopefully
easier to browse.
On the website, there is a manual for Ray.
Sébastien
1.4.0
2011-05-30
* A built-in scaffolder is now available -- Thanks to Dr.
Jean-Francois Pombert (University of British Columbia) for the
suggestion.
* The maximum number of libraries is now 499 instead of 250.
* The number of seeds is now divided by 2 to speed up their
extension.
* Fixed a bug in the depth first search that leaded to vertices
having no coverage values.
* Removed the configure script, now Ray must be compiled with the
provided Makefile.
* Added a switch to enable the profiler: -run-profiler
* Added a switch to debug seed generation: -debug-seeds
* Added a switch to debug bubble detection: -debug-bubbles
* Added a switch to show memory usage: -show-memory-usage
* Added a switch to show the ending context of extensions:
-show-ending-context
* Devised a new algorithm that finds the peak coverage, minimum
coverage and repeat coverage in distributions.
* Ray now writes the peak, minimum and repeat coverages to a file.
* Ray now writes the statistics for libraries to a file.
* Fixed a bug that disallowed mixing manual and automatic
detection of outer distances.
* Ray now writes the statistics for seed lengths to a file.
* Devised a new algorithm that computes longer seeds to bootstrap
assemblies.
* Slave modes, master modes and MPI tags are generated with macros
for method prototypes, enumerations and assignments in arrays.
* Added some changes for Microsoft Windows compatibility. Thanks
to Hannes Pouseele (Applied Maths, Inc.) for some suggestions.
* Added instructions regarding mpic++ and CXX environment
variable. Thanks to Dr. Harry Mangalam from UC Irvice for
pointing that out.
* Changed the merger behavior for ends of contigs.
* Added a script to validate scaffolds.
Dear Ray users,
Ray 1.4.0 is now available.
The most significant change is the built-in scaffolder.
The second most significant change is the new algorithm that finds
assembly seeds.
Also, I added a lot of output files in Ray.
They are listed here:
Finally, our new website http://denovoassembler.sf.net is hopefully
easier to browse.
On the website, there is a manual for Ray.
Sébastien
1.4.0
2011-05-30
* A built-in scaffolder is now available -- Thanks to Dr.
Jean-Francois Pombert (University of British Columbia) for the
suggestion.
* The maximum number of libraries is now 499 instead of 250.
* The number of seeds is now divided by 2 to speed up their
extension.
* Fixed a bug in the depth first search that leaded to vertices
having no coverage values.
* Removed the configure script, now Ray must be compiled with the
provided Makefile.
* Added a switch to enable the profiler: -run-profiler
* Added a switch to debug seed generation: -debug-seeds
* Added a switch to debug bubble detection: -debug-bubbles
* Added a switch to show memory usage: -show-memory-usage
* Added a switch to show the ending context of extensions:
-show-ending-context
* Devised a new algorithm that finds the peak coverage, minimum
coverage and repeat coverage in distributions.
* Ray now writes the peak, minimum and repeat coverages to a file.
* Ray now writes the statistics for libraries to a file.
* Fixed a bug that disallowed mixing manual and automatic
detection of outer distances.
* Ray now writes the statistics for seed lengths to a file.
* Devised a new algorithm that computes longer seeds to bootstrap
assemblies.
* Slave modes, master modes and MPI tags are generated with macros
for method prototypes, enumerations and assignments in arrays.
* Added some changes for Microsoft Windows compatibility. Thanks
to Hannes Pouseele (Applied Maths, Inc.) for some suggestions.
* Added instructions regarding mpic++ and CXX environment
variable. Thanks to Dr. Harry Mangalam from UC Irvice for
pointing that out.
* Changed the merger behavior for ends of contigs.
* Added a script to validate scaffolds.
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