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[page edited on August, 24th, 2020]
Screen Shot 2014-08-12 at 15.15.44

Mapsembler2 is not maintained anymore

Sadly, we have no more man power to maintain and to update Mapsembler2.  The last (2014) version is this one:  mapsembler2_2.2.4.

Many bug fixes, new features, and optimizations are expected. Any help would be warmly welcome!

Mapsembler2 description and possible usages:

Mapsembler2 is a targeted assembly software. It takes as input any number of NGS raw read set(s) (fasta or fastq, gzipped or not) and a set of input sequences (starters). For each starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice. Mapsembler2 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 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 · Check the presence / absence and quantify RNA seq splicing events. Check the presence/absence of SNPs or structural variants, …

What’s new in Mapsembler2?

Two main novelties are implemented in mapsembler2:

  • The Minia data structure is now used for indexing reads. For the price of using a few Gigabytes RAM, Mapsembler2 is much faster as it reads the read files only once.
  • The starters are only extended. Mapsembler does not search for all (possibly numerous) sub-starters.
  • An ad hoc visualization interface is proposed.

Video Tutos

Mapsembler2 install and use:
Mapsembler2 Graph of Sequence Viewer:

Download Mapsembler2:

Please read and accept the GNU Affero General Public License before use and diffusion. Any feedback and comment is warmly encouraged.

Actual version: mapsembler2_2.2.4


Download Mapsembler1 – from old web site: Alcovna

Please read and accept the License before use and diffusion. Any feedback and comment is warmly encouraged. The last mapsembler1 release may be downloaded here:  mapsembler_1.3.21 (beta version).

Download Graph of Sequence Viewer for Galaxy:

GSV for Galaxy v1.0
GSV for Galaxy (beta version)


For any questions, contact us: or on Biostars