Novoalign

Our primary product 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.

• No limit of 2 mismatches per read, aligns with up to 8 or more mismatches per read, up to 16 on paired end reads.

• Gapped alignment on single end reads and paired end reads. Gaps up to 7bp on single end reads, even longer on paired end reads.
• Uses base qualities at all steps in the alignment for greater accuracy.
• Native SAM/BAM alignment output format
• Single pass alignment for Bisulphite treated DNA.
• Base Quality calibration for greater accuracy and extra reads. Do you still need the phiX control lane?
• 3'  & 5' Adapter stripping for short fragments (eg. miRNA) & PCR adapters
• Pooled samples with indexing using Novobarcode.
• Excellent performance on long reads from the Illumina GA II
• Cluster-aware message passing interface (MPI) and multithreaded versions
• Align Illumina Mate pairs including: mixed pairs/mates, and split ends when read includes circularisation junction
• Align 454 paired end reads

NovoalignCS

 Implements key functions of Novoalign for Colour Space reads from ABI Life Sciences SOLiD system.

• Probably the most accurate colour space aligner available today.