Difference between revisions of "Mosaik"

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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}}
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==System Variables==
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* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 
* HPC_MOSAIK_BIN - executable file directory
 
* HPC_MOSAIK_BIN - executable file directory
 
{{#if: {{#var: exe}}|==How To Run==
 
{{#if: {{#var: exe}}|==How To Run==

Revision as of 19:12, 10 August 2012

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_{{#uppercase:mosaik}}_DIR - installation directory
  • HPC_MOSAIK_BIN - executable file directory