Novocraft Technologies is a bioinformatics company specializing in

  • the development of fast and accurate tools for next-generation sequencing (NGS) analysis and,
  • provision of bioinformatics services where our team of experts analyse your NGS data for you.



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


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

  • Probably the most accurate colour space aligner available today.







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Last Update: 20 Oct 2014 05:13 AM