Difference between revisions of "Mosaik"

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(Created page with "__NOTOC__ __NOEDITSECTION__ Category:Software <!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in template calls Required variab...")
 
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[[Category:Software]]
 
[[Category:Software]]
<!-- ########  Template Configuration ######## -->
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{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|mosaik}}
 
|{{#vardefine:app|mosaik}}
|{{#vardefine:url|http://code.google.com/p/mosaik-aligner/t}}
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|{{#vardefine:url|http://code.google.com/p/mosaik-aligner/}}
<!--Compiler and MPI settings - OPTIONAL -->
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
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<!--Description-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
        MOSAIK is a reference-guided assembler comprising of four main modular programs:
 
  
        MosaikBuild
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MOSAIK is a reference-guided assembler comprising of four main modular programs:
        MosaikAligner
 
        MosaikSort
 
        MosaikText
 
  
        MosaikBuild converts various sequence formats into Mosaik’s native read
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* MosaikBuild
        format. MosaikAligner pairwise aligns each read to a specified series
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* MosaikAligner
        of reference sequences. MosaikSort resolves paired-end reads and sorts
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* MosaikSort
        the alignments by the reference sequence coordinates. Finally,
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* MosaikText
        MosaikText converts alignments to different text-based formats.
 
  
        At this time, the workflow consists of supplying sequences in FASTA,
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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.
        FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing
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        results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or
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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.
        the Illumina ELAND formats.
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<!--Modules-->
<!--Location-->
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==Required Modules==
{{App_Location|app={{#var:app}}|{{#var:ver}}}}
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[[Modules|modules documentation]]
<!-- -->
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===Serial===
{{#if: {{#var: mod}}|==Running the application using modules==
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*{{#var:app}}
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
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==System Variables==
* HPC_MOSAIK_BIN - executable file directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory.
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* HPC_MOSAIK_BIN - executable file directory.
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* HPC_MOSAIK_NET - network file directory.
 +
* MOSAIK_TMP - default temporary file directory. Note that HiPerGator2 nodes are diskless, so MOSAIK_TMP must not be set to /tmp.
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
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If you would like to use the provided network files with MosaikAligner use the $HPC_MOSAIK_NET variable for the location of network file directory. E.g.
 +
MosaikAligner -annpe $HPC_MOSAIK_NET/2.1.26.pe.100.0065.ann \
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-annse $HPC_MOSAIK_NET/2.1.26.se.100.005.ann -in ...
 +
|}}
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
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{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==

Latest revision as of 21:23, 6 December 2019

Description

mosaik website  

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.

Required Modules

modules documentation

Serial

  • mosaik

System Variables

  • HPC_MOSAIK_DIR - installation directory.
  • HPC_MOSAIK_BIN - executable file directory.
  • HPC_MOSAIK_NET - network file directory.
  • MOSAIK_TMP - default temporary file directory. Note that HiPerGator2 nodes are diskless, so MOSAIK_TMP must not be set to /tmp.

How To Run

If you would like to use the provided network files with MosaikAligner use the $HPC_MOSAIK_NET variable for the location of network file directory. E.g.

MosaikAligner -annpe $HPC_MOSAIK_NET/2.1.26.pe.100.0065.ann \
-annse $HPC_MOSAIK_NET/2.1.26.se.100.005.ann -in ...