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.