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[edit] News

2009-02-01: Mosaik 0.9.0891 has been released!

[edit] Overview

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.

At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing assembly files (phrap ace and GigaBayes gig formats) which can be viewed with utilities such as consed or EagleView.

[edit] What makes MOSAIK different?

Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Additionally, our program goes beyond producing pairwise alignments and produces reference-guided assemblies with gapped alignments. These features make it ideal for downstream single nucleotide polymorphism (SNP) and short insertion/deletion (INDEL) discovery.

MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, Linux/x86, Linux/Itanium2, and Sun Solaris/UltraSPARC operating systems. Other platforms can easily be supported upon request.

MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor.

MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope.

[edit] 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, 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

[edit] Current Documentation

In addition to discussing how to run MOSAIK, our documentation also covers fundamental alignment concepts, tips on improving performance, and how to access our file formats natively.

[edit] Release 0.9.891 (2009-02-01)

Registered users can download the MOSAIK distribution here:

NEW! Not a registered user yet? Sign up here!

[edit] Found a bug?

Found a bug in MOSAIK? Please report it on our bug tracking website for quicker bug resolution.

[edit] Unified Release

You can download the unified release consisting of PyroBayes, Mosaik, and GigaBayes for 32-bit and 64-bit Linux here.

[edit] Developers

Michael Strömberg

Retrieved from "http://bioinformatics.bc.edu/marthlab/Mosaik"