MOSAIK
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Application data |
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| Created by | Strömberg M |
|---|---|
| Principal bioinformatics method(s) | Sequence assembly |
| Created at | The Marth Lab, Department of Biology, Boston College, Massachusetts |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ, Illumina Bustard, Gerald, SRF |
| Output format(s) | gig, ACE, Axt, BED, eland, SAM, BAM |
| Programming language(s) | C++ |
| Licence | Commercial, GPLv2 |
| Operating system(s) | Windows, Linux, Mac OS X |
Summary: Reference guided aligner/assembler.
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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
Links
References
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