View source for MOSAIK

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[[Category:Software]]
{|<!--Main settings - REQUIRED-->
|{{#vardefine:app|mosaik}}
|{{#vardefine:url|http://code.google.com/p/mosaik-aligner/}}
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
|{{#vardefine:policy|}} <!--Enable policy section -->
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:citation|1}} <!--Enable Reference/Citation section -->
|}
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<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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.
<!--Modules-->
==Required Modules==
[[Modules|modules documentation]]
===Serial===
*{{#var:app}}
==System Variables==
* HPC_{{uc:{{#var:app}}}}_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.
{{#if: {{#var: exe}}|==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 ...
|}}
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
{{#if: {{#var: testing}}|==Performance==
WRITE PERFORMANCE TESTING RESULTS HERE|}}
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
{{#if: {{#var: citation}}|==Citation==
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]
|}}