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[edit] News

2009-10-14: Mosaik 1.0 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's new?

  1. The overall alignment speed is much quicker now due to a banded Smith-Waterman algorithm implementation by Wan-Ping Lee. Longer Roche 454 reads align much quicker than before.

  2. Alignment qualities have been studied heavily and two separate logistic regression models were created to increase the accuracy and usefulness of our alignment qualities.

  3. A local alignment search option has been added to help rescue mates in paired-end/mate-pair reads that may be missing due to highly repetitive regions in the genome.

  4. SOLiD support has finally come of age. MOSAIK imports and aligns SOLiD reads in colorspace, but now seamlessly converts the alignments back into basespace. No more downstream bioinformatics headaches.

  5. Robust support for the SAM & BAM alignment file formats.

  6. The command line parameters have been cleaned up and sensible default parameters have been chosen. This cuts down the ridiculously long command-lines to simply specifying an input file and an output file in most cases.

  7. In the last software release, the 32-bit Linux and Mac OS X distributions had some problems. Those issues have been resolved now. You can call off the hitmen :-)

[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, 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

[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 1.0 (2009-10-14)

Registered users receive updates when the new tools are released by the Marth Lab. 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. The unified release is currently out of sync and still contains the older version of MOSAIK. A new unified release is expected shortly.

[edit] Finally Open Source!

By popular demand, MOSAIK is now dual licensed under the GPL 2.0+ and via a commercial license available from the Marth Lab. The source code is availabe on our Google Code Hosting site:

http://code.google.com/p/mosaik-aligner

[edit] Questions about MOSAIK

Do you have any questions concerning MOSAIK? Engage the sequencing community by posting them to the SEQanswers Bioinformatics forum.

[edit] Developers

Michael Strömberg
Wan-Ping Lee

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