Paper Mapsembler
The mapsembler paper was accepted to BMC bioinformatics.
Here is a proper formatting:
Peterlongo, P., & Chikhi, R. (2012). Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinformatics, 13(1), 48. doi:10.1186/1471-2105-13-48. 
KisSplice paper
Kissplice will soon be presented during the Recomb-seq workshop.
“KisSplice: de-novo calling alternative splicing events from RNA-seq data”
The alcovna team
The Alcovna team grow up last two years. At the very beginning of the story it was composed by:
- Pise, Italie:
- Roberto Grossi
- Nadia Pisanti
- Lyon, Equipe Projet INRIA Bamboo:
- Vincent Lacroix
- Marie-France Sagot
- Toulouse (visualisation):
- Fabien Jourdan
- Rennes, Equipe Projet INRIA Symbiose:
- Pierre Peterlongo
Nowadays the project welcome new collaborators:
- Lyon:
- Gustavo Sacomoto
- Janice Kielbassa
- Rennes:
- Claire Lemaitre
- Pavlos Antoniou
- Rayan Chikhi
- Raluca Uricaru
Mapsembler: Bug fixed
In version 1.3.16 (available from the mapsembler page) a memory bug is fixed.
This bug appeared sometimes when starters were not read coherents. The output was the following:
“Read coherence: Index starters Check read coherence…
[...................................................................................................] mapping reads
[.cannot allocate memory for variable substarters, exit ] sub-starters generation “
Mapsembler 1.3.15 available
Download and general information on the mapsembler page
- Optimization of the sub-starter generation
- Cleaning of the graph (remove deadend small paths)
mapsembler 1.3.12 available
Available for download on the mapsembler page
Novelties:
- some bug fixed (in particular about the substarter generation)
- possibility to obtain the intermediate results after stopping the program (CTRL-C) before the end of the process
- possibility (option -g) to get a fasta file containing the reads that were mapped on starter, substarters or their extensions.
Mapsembler 1.3.7 available
A new mapsembler version is available. Novelties:
- Three modes available (replacing the -g option):
- -m 0: no branching (equivalent: no -g option in the previous release)
- -m 1: accepts small divergences during extensions. Output a fasta file.
- -m 2: ouput a graph (equivalent: -g option in the previous release)
- [BETA] New graph format: possibility to require graphml format, readable for instance by gephi: http://gephi.org/ (simply use option -m2 and -o file_name.graphml)
- Outputs the read coverage, position per position. (-f option)
Download : Mapsembler page
Mapsembler download
Please read and accept the License before use and diffusion.
Any feedback and comment is warmly encouraged.
Mapsembler downloads can be found in the mapsembler page.
New mapsembler release
A new mapsembler release (1.3.5) is available. It proposes options allowing the checking and the extension of a limited fragment of the starters.
- Option -E <value>: enables to limit the read coherence checking to a prefix and/or a suffix of each starter
- Option -l: extend starters on their left direction only
- Option -r: extend starters on their right direction only
Please check the mapsembler page for download.
