Introduction
Novocraft specialises in the development of fast and accurate tools for comparative genomics. 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 whilst performing at the same or better speed than aligners that are limited to two mismatches and no insert or deletes.
Key Features of Novoalign
- 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.
- 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' Adapter stripping for miRNA.
- 5' Adapter stripping for Nimblegen Sequence Capture Arrays.
- Pooled samples with indexing using Novobarcode.
- Excellent performance on long reads from the Illumina GA II
"NovoAlign is the most accurate aligner to date" Heng Li, Author of MAQ
Citations & References
Genome-wide analysis of allelic expression imbalance in human primary cells by high throughput transcriptome resequencing
Graham A. Heap, Jennie H.M. Yang, Kate Downes, Barry C. Healy, Karen A. Hunt, Nicholas Bockett, Lude Franke, Patrick C. Dubois, Charles A. Mein, Richard J. Dobson, Thomas J. Albert, Matthew J. Rodesch, David G. Clayton, John A. Todd, David A. van Heel, and Vincent Plagnol
Human Molecular Genetics, doi:10.1093/hmg/ddp473
Abundant primary piRNAs, endo-siRNAs and microRNAs in a Drosophila ovary cell line
Nelson Lau1,Nicolas Robine,Raquel Martin, Wei-Jen Chung,Yuzo Niki, Eugene Berezikov and Eric C. Lai
Genome Research, Published in Advance June 18, 2009, doi: 10.1101/gr.094896.109
Digital transcriptome profiling using selective hexamer priming for cDNA synthesis
Armour CD, Castle JC, Chen R, Babak T, Loerch P, Jackson S, Shah JK, Dey J, Rohl CA, Johnson JM, Raymond CK.
Nat Methods. 2009 Sep;6(9):647-9. Epub 2009 Aug 9
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples.
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, and Ding L.
Bioinformatics. 2009 Jun 19.
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
Peter D. Keightley, Urmi Trivedi, Marian Thomson, Fiona Oliver, Sujai Kumar and Mark L. Blaxter
Genome Res. 2009. Volume 19: 1195-1201
Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection
Daniel S Herman, G Kees Hovingh, Oleg Iartchouk, Heidi L Rehm, Raju Kucherlapati, J G Seidman & Christine E Seidman
Nature Methods 6, 507 - 510 (2009)
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
Sander Granneman, Grzegorz Kudla, Elisabeth Petfalski, and David Tollervey
PNAS 2009 106: 9613-9618.