ARC Alcovna

but hopefully it is followed by the

ANR Colib’read

Here is the web site: http://colibread.inria.fr

WARNING: ALL NEW DEVELOPMENTS WILL BE STORED ON THE COLIB’READ WEB PAGE

We are pleased to announce that the french ANR (Agence Nationnale de la Recherche) project Colib’read which aims at pursuing the Alcovna objectives had been founded.

Thanks to this project the already developed tools will be strengthen  while new ideas will be explored.

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.

See http://alcovna.genouest.org/job-offer/

Kissplice was presented during the Recomb-seq workshop.

It is now published in BMC Bioinformatics: “KisSplice: de-novo calling alternative splicing events from RNA-seq data”.

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

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 “

Download and general information on the mapsembler page

• Optimization of the sub-starter generation
• Cleaning of the graph (remove deadend small paths)

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.

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