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mosaik website  

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

MosaikBuild MosaikAligner MosaikBuild converts various sequence formats into Mosaik’s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs.

At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format.

Environment Modules

Run module spider mosaik to find out what environment modules are available for this application.

System Variables

  • HPC_MOSAIK_DIR - installation directory
  • HPC_MOSAIK_BIN - executable directory
  • HPC_MOSAIK_NET - network file directory
  • MOSAIK_TMP - directory for temporary files


If you publish research that uses mosaik you have to cite it as follows: