Difference between revisions of "Novoalign"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "")
 
(8 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]][[Category:Bioinformatics]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]]
 
+
{|<!--Main settings - REQUIRED-->
{|
 
<!--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}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
 
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
Line 40: Line 34:
 
===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}}
 +
 +
'''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
Line 58: Line 62:
 
WRITE CITATION HERE
 
WRITE CITATION HERE
 
|}}
 
|}}
 +
=Validation=
 +
* Validated 4/5/2018

Latest revision as of 17:19, 19 August 2022

Description

novoalign website  

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

modules documentation

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