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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. Finally,
       MosaikText converts alignments to different text-based formats.
       At this time, the workflow consists of supplying sequences in FASTA,
       FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing
       results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or
       the Illumina ELAND formats.

Template:App Location

Running the application using modules

To use mosaik with the environment modules system at HPC the following commands are available:

Get module information for mosaik:

$module spider mosaik

Load the default application module:

$module load mosaik

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_MOSAIK_DIR - directory where mosaik is located.
  • HPC_MOSAIK_BIN - executable file directory