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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, MosaikAssembler parses the sorted alignment archive and produces a multiple sequence alignment which is then saved into an assembly file format.
=== Features === * aligns a large range of read lengths- from short Illumina reads to medium 454 reads to long legacy Sanger reads
* co-assembly - can create an assembly with multiple sequencing technologies (Illumina, Roche 454, AB SOLiD, Helicos, and Sanger)
