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mosaik website  

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

  • MosaikBuild
  • MosaikAligner
  • MosaikSort
  • MosaikText

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.

Required Modules

modules documentation


  • mosaik

System Variables

  • HPC_MOSAIK_DIR - installation directory.
  • HPC_MOSAIK_BIN - executable file directory.
  • HPC_MOSAIK_NET - network file directory.
  • MOSAIK_TMP - default temporary file directory. Note that HiPerGator2 nodes are diskless, so MOSAIK_TMP must not be set to /tmp.

How To Run

If you would like to use the provided network files with MosaikAligner use the $HPC_MOSAIK_NET variable for the location of network file directory. E.g.

MosaikAligner -annpe $HPC_MOSAIK_NET/ \
-annse $HPC_MOSAIK_NET/ -in ...