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. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_MOSAIK_BIN - executable file directory. | * HPC_MOSAIK_BIN - executable file directory. | ||
* HPC_MOSAIK_NET - network file directory. | * HPC_MOSAIK_NET - network file directory. | ||
Revision as of 19:01, 10 June 2022
Description
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: