Novoalign

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Description

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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. Template:App Location

Available versions

  • 2.07.15 - free version (academic, non-profit use; limited functionality and performance)

Running the application using modules

To use novoalign with the environment modules system at HPC the following commands are available:

Get module information for novoalign:

$module spider novoalign

Load the default application module:

$module load novoalign

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_NOVOALIGN_DIR - directory where novoalign is located.
  • HPC_NOVOALIGN_BIN - executable directory
  • HPC_NOVOALIGN_DOC - documentation directory