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

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

@@ Line 2: / Line 2: @@
 __NOEDITSECTION__
 [[Category:Software]][[Category:Bioinformatics]]
-<!-- ########  Template Configuration ######## -->
+{|<!--Main settings - REQUIRED-->
-<!--Edit definitions of the variables used in template calls
-Required variables:
-app - lowercase name of the application e.g. "amber"
-url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
-{|
-<!--Main settings - REQUIRED-->
 |{{#vardefine:app|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" -->
-<!--Choose sections to enable - OPTIONAL-->
-|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
 |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
@@ Line 44: / Line 29: @@
 requested by the software manufacturer [http://www.novocraft.com/wiki/tiki-view_faq.php?faqId=1#q23 in Novoalign FAQ].
-==Available versions==
+<!--Modules-->
-* 2.07.15 - free version (academic, non-profit use; limited functionality and performance)
+==Required Modules==
-<!-- -->
+[[Modules|modules documentation]]
-{{#if: {{#var: mod}}|==Execution Environment and Modules==
+===Serial===
-{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+*{{#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_DOC - documentation directory
@@ Line 57: / Line 52: @@
 {{#if: {{#var: pbs}}|==PBS Script Examples==
 See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
-{{#if: {{#var: policy}}|==Usage policy==
+{{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
 {{#if: {{#var: testing}}|==Performance==
@@ Line 67: / Line 62: @@
 WRITE CITATION HERE
 |}}
+=Validation=
+* Validated 4/5/2018

Difference between revisions of "Novoalign"