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MOSAIK is a reference-guided assembler comprising of four main modular programs:

  • MosaikBuild -- converts various sequence formats into Mosaik’s native read format
  • MosaikAligner -- pairwise aligns each read to a specified series of reference sequences
  • MosaikSort -- resolves paired-end reads and sorts the alignments by the reference sequence coordinates
  • MosaikAssembler -- parses the sorted alignment archive and produces a multiple sequence alignment which is then saved into an assembly file format


open-source under the terms of the GPL 2.0+ license and the MIT licence


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of mosaik and load default version of mosaik as

module avail mosaik/ # list available modules
module load mosaik   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail mosaik

and choose explicit version you want to use.

1. Running the application -- Batch mode:

  • prepare the job description script -- use a general skeleton supplemented by the following lines:
# load the application module
module add mosaik-2.1

# run the computation
MosaikAligner -in <filename> -out <filename> -ia <filename>
  • pass the job description file to the scheduler together with (at least) the requested number of processors and requested amount of memory
$ qsub -l nodes=1:ppn=X -l mem=Yg

2. Running the application -- Interactive mode:

  • ask the scheduler for an interactive job having a single node and a desired number of processors (ppn attribute) reserved
$ qsub -I -l nodes=1:ppn=X -l mem=Yg
Note: Do not forget to apppropriately set the amount of requested memory (mem attribute) and/or another job requirements
  • load the Mosaik module
$ module add mosaik-2.1
  • prepare the input files and run the computation
$ MosaikAligner -in <filename> -out <filename> -ia <filename>