Difference between revisions of "Mosaik"

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|{{#vardefine:url|http://code.google.com/p/mosaik-aligner/}}
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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.
 
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.
 
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<!--Modules-->
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==Required Modules==
 
==Required Modules==
 
[[Modules|modules documentation]]
 
[[Modules|modules documentation]]
 
===Serial===
 
===Serial===
 
*{{#var:app}}
 
*{{#var:app}}
* HPC_MOSAIK_BIN - executable file directory
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==System Variables==
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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.
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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.
 
{{#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.
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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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|}}
 
{{#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.|}}

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 ...