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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


  • Module mosaik-1.1: Mosaik version 1.1, 64-bit
  • Module mosaik-2.1: Mosaik version 2.1, 64-bit


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>



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

Supported platforms


Program administrator