Difference between revisions of "MOSAIK"

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(Created page with "Category:SoftwareCategory:BiologyCategory:BioinformaticsCategory:Short Read Alignment {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|mosaik}} |{{#vardefine...")
 
 
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[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:Short Read Alignment]]
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__NOTOC__
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{|<!--CONFIGURATION: REQUIRED-->
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[[Category:Software]][[Category:Biology]][[Category:Alignment]]
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{|<!--Main settings - REQUIRED-->
 
|{{#vardefine:app|mosaik}}
 
|{{#vardefine:app|mosaik}}
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|{{#vardefine:url|https://code.google.com/archive/p/mosaik-aligner/}}
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|{{#vardefine:url|http://code.google.com/p/mosaik-aligner/}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
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<!--Description-->
 
<!--Description-->
 
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
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MOSAIK is a reference-guided assembler comprising of two main modular programs:
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MOSAIK is a reference-guided assembler comprising of four main modular programs:
  
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MosaikBuild
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* MosaikBuild
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MosaikAligner
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* MosaikAligner
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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 and produces BAMs as outputs.
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* MosaikSort
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* MosaikText
  
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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 BAM format.
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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.
  
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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.
 
<!--Modules-->
 
<!--Modules-->
 
==Environment Modules==
 
==Environment Modules==
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
==System Variables==
 
==System Variables==
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* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
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* HPC_MOSAIK_BIN - executable file directory.
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* HPC_{{#uppercase:{{#var:app}}}}_NET - network file directory
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* HPC_MOSAIK_NET - network file directory.
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* MOSAIK_TMP - directory for temporary files
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* MOSAIK_TMP - default temporary file directory. Note that HiPerGator2 nodes are diskless, so MOSAIK_TMP must not be set to /tmp.
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{{#if: {{#var: exe}}|==How To Run==
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<!--Configuration-->
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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.
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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 ...
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|}}
 
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
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|}}
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
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{{#if: {{#var: exe}}|==Additional Information==
 
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 
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|}}
 
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{{#if: {{#var: job}}|==Job Script Examples==
 
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See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
 
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|}}
 
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{{#if: {{#var: policy}}|==Usage Policy==
 
{{#if: {{#var: policy}}|==Usage Policy==
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
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WRITE USAGE POLICY HERE (Licensing, usage, access).
 
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|}}
 
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{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
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WRITE PERFORMANCE TESTING RESULTS HERE|}}
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
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|}}
 
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{{#if: {{#var: faq}}|==FAQ==
 
{{#if: {{#var: faq}}|==FAQ==
 
*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
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<!--Citation-->
 
 
{{#if: {{#var: citation}}|==Citation==
 
{{#if: {{#var: citation}}|==Citation==
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If you publish research that uses {{#var:app}} you have to cite it as follows:
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If you publish research that uses {{{app}}} you have to cite it as follows:
  
 
[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581 http://dx.plos.org/10.1371/journal.pone.0090581]
 
[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581 http://dx.plos.org/10.1371/journal.pone.0090581]
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|}}
 
|}}
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{{#if: {{#var: installation}}|==Installation==
 
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
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__NOTOC____NOEDITSECTION__
 

Latest revision as of 11:59, 19 August 2022

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.

Environment Modules

Run module spider mosaik to find out what environment modules are available for this application.

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 ...



Citation

If you publish research that uses {{{app}}} you have to cite it as follows:

http://dx.plos.org/10.1371/journal.pone.0090581

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=MOSAIK&oldid=25509"