Difference between revisions of "Novoalign"
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__NOEDITSECTION__ | __NOEDITSECTION__ | ||
[[Category:Software]][[Category:Bioinformatics]] | [[Category:Software]][[Category:Bioinformatics]] | ||
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| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|novoalign}} | |{{#vardefine:app|novoalign}} | ||
|{{#vardefine:url|http://www.novocraft.com/main/page.php?s=novoalign}} | |{{#vardefine:url|http://www.novocraft.com/main/page.php?s=novoalign}} | ||
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|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | '''Note:''' Multiple software packages are made available via the novoalign module: novocraft (Novoalign), novoalignCS, novomethyl, and novosort. | ||
| + | ===Parallel (MPI)=== | ||
| + | * intel | ||
| + | * openmpi | ||
| + | *{{#var:app}} | ||
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| + | '''Note:''' Multiple software packages are made available via the novoalign module: novoalignMPI and novoalignCSMPI. | ||
| + | |||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_NOVOALIGN_BIN - executable directory | * HPC_NOVOALIGN_BIN - executable directory | ||
* HPC_NOVOALIGN_DOC - documentation directory | * HPC_NOVOALIGN_DOC - documentation directory | ||
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WRITE CITATION HERE | WRITE CITATION HERE | ||
|}} | |}} | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 21:22, 6 December 2019
Description
Novoalign is a highly accurate program for mapping next-generation sequencing reads to a reference database. It is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.
Limited functionality and single-threaded performance are available without a paid license. Novoalign must only be used for academic/non-profit research and the results of the analyses must published in peer-reviewed journals as requested by the software manufacturer in Novoalign FAQ.
Required Modules
Serial
- novoalign
Note: Multiple software packages are made available via the novoalign module: novocraft (Novoalign), novoalignCS, novomethyl, and novosort.
Parallel (MPI)
- intel
- openmpi
- novoalign
Note: Multiple software packages are made available via the novoalign module: novoalignMPI and novoalignCSMPI.
System Variables
- HPC_NOVOALIGN_DIR - installation directory
- HPC_NOVOALIGN_BIN - executable directory
- HPC_NOVOALIGN_DOC - documentation directory
Validation
- Validated 4/5/2018