Difference between revisions of "Mosaik"

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        MOSAIK is a reference-guided assembler comprising of four main modular programs:
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MOSAIK is a reference-guided assembler comprising of four main modular programs:
  
        MosaikBuild
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* MosaikBuild
        MosaikAligner
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* MosaikAligner
        MosaikSort
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MosaikSort
        MosaikText
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* MosaikText
  
        MosaikBuild converts various sequence formats into Mosaik’s native read
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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, MosaikText converts alignments to different text-based formats.
        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,
 
        MosaikText converts alignments to different text-based formats.
 
  
        At this time, the workflow consists of supplying sequences in FASTA,
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At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or the Illumina ELAND formats.
        FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing
 
        results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or
 
        the Illumina ELAND formats.
 
 
<!--Location-->
 
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Revision as of 04:41, 28 October 2011

Description

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MOSAIK is a reference-guided assembler comprising of four main modular programs:

  • MosaikBuild
  • MosaikAligner

• MosaikSort

  • MosaikText

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, MosaikText converts alignments to different text-based formats.

At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or the Illumina ELAND formats. Template:App Location

Running the application using modules

To use mosaik with the environment modules system at HPC the following commands are available:

Get module information for mosaik:

$module spider mosaik

Load the default application module:

$module load mosaik

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_MOSAIK_DIR - directory where mosaik is located.
  • HPC_MOSAIK_BIN - executable file directory