MOSAIK: Difference between revisions
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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== | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_NET - network file directory | ||
* MOSAIK_TMP - directory for temporary files | * MOSAIK_TMP - directory for temporary files | ||
Revision as of 21:21, 6 December 2019
Description
MOSAIK is a reference-guided assembler comprising of two main modular programs:
MosaikBuild MosaikAligner 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.
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.
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 directory
- HPC_MOSAIK_NET - network file directory
- MOSAIK_TMP - directory for temporary files
Citation
If you publish research that uses mosaik you have to cite it as follows:
http://dx.plos.org/10.1371/journal.pone.0090581