ARC Alcovna

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

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.

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.

Some small modification on the in/out of the kisSnpCheckReads tool were uploaded today. Check the kisSnp page for a unpdate.

A new version (lighter and faster) of kisSnp is available, please check the dedicated page for download and instructions for use.

Citation:  Mapsembler, targeted assembly of larges genomes on a desktop computer Peterlongo P., Chikhi R. N° RR-7565 (2011) [inria-00577218 - version 1]

Documents:

• mapsembler_slides
• usersguide
• research report