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