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MOSAIK is a reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into MOSAIK’s native 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.