Difference between revisions of "Mosaik"
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Moskalenko (talk | contribs) m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}") |
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|{{#vardefine:app|mosaik}} | |{{#vardefine:app|mosaik}} | ||
| − | |{{#vardefine:url|http://code.google.com/p/mosaik-aligner/ | + | |{{#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. | ||
| − | + | <!--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 | + | ==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: {{#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== | {{#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 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
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 ...
