MOSAIK v2.1.73 (Reference guided aligner/assembler)
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, MosaikAssembler parses the sorted alignment archive and produces a multiple sequence alignment which is then saved into an assembly file format.
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)
reference-guided aligner - use an entire genome as a reference when aligning reads
gapped alignment - especially useful for insertion / deletion (indel) detection
fast - aligns 2 million Illumina 36 bp reads against the full human genome in 8 minutes using 8 processor cores