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.
To run this software interactively in a Linux environment run the commands:
module load novoalign
novoindex indexfile sequencefiles
novoalign -d indexfile

For documentation, run a command without parameters, or refer to the Novoalign homepage.

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