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Mar 29 12

Paper Mapsembler

by Pierre Peterlongo

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.

Mar 20 12

Job Offer: Postdoc in algorithmics for NextGen Sequencing data

by Pierre Peterlongo

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

Feb 14 12

KisSplice paper

by Pierre Peterlongo

Kissplice will soon be presented during the Recomb-seq workshop.

“KisSplice: de-novo calling alternative splicing events from RNA-seq data”

Dec 6 11

The alcovna team

by Pierre Peterlongo

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
Oct 17 11

Mapsembler: Bug fixed

by Pierre Peterlongo

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

Aug 31 11

Mapsembler 1.3.15 available

by Pierre Peterlongo

Download and general information on the mapsembler page

  • Optimization of the sub-starter generation
  • Cleaning of the graph (remove deadend small paths)
Jul 26 11

mapsembler 1.3.12 available

by Pierre Peterlongo

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.
Apr 22 11

Mapsembler 1.3.7 available

by Pierre Peterlongo

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

Apr 22 11

Mapsembler download

by Pierre Peterlongo

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.

Apr 6 11

New mapsembler release

by Pierre Peterlongo

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.