Skip to content




[PAGE UPDATED on April,04 2012 - Fixed a mapsembler bug on mac]

Description and possible usages:

Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
Mapsembler may be used for (not limited to):

· Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
· Checks if a gene (input as starter) has an homolog in a set of reads
· Checks if a known enzyme is present in a metagenomic NGS read set.
· Enrich unmappable reads by extending them, possibly making them mappable
· Checks what happens at the extremities of a contig
· Remove contaminants or symbiont reads from a read set


The last mapsembler release may be downloaded here:  mapsembler_1.3.21 (beta version).
Please read and accept the License before use and diffusion.
Any feedback and comment is warmly encouraged. You may also subscribe to our mailing list to receive notifications of updates.

Mailing list:




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.


  • [04/04/2012] mapsembler_1.3.21
    • Corrected two bug related to mac OS.
  • [23/03/2012] mapsembler_1.3.19 [BETA]
    • Improved the hash table
  • [14/02/2012] – mapsembler_1.3.17 [STABLE]
    • Enhanced various features
  • [17/10/2011] – mapsembler_1.3.16
    • Fixes a bug related to memory
  • [31/08/2011] - mapsembler_1.3.15
    • Better cleaning of the graph
    • Optimization of sub-starter generation (time and memory)
  • [26/07/2011] - mapsembler_1.3.12[22/04/2011] – mapsembler_1.3.7: new mode for extending more – bug fixed – output graphml format – provides full coverage
    • 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.
  • [07/04/2011] – mapsembler_1.3.5.1: increase the possible number of sub-starters
  • [06/04/2011] – mapsembler_1.3.5: adding restriction options.
  • [03/2011] – mapsembler_1.3.4: Base version

The mapsembler team.