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Short description:
Please summarise the application in a few sentences. Avoid links here. Reference guided aligner/assembler.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Sequence assembly
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
The Marth Lab, Department of Biology, Boston College, Massachusetts
MOSAIK is a reference-guided assembler comprising of four main modular programs: * MosaikBuild * MosaikAligner * MosaikSort * MosaikAssembler. 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) * 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
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