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DNAStar's Next-Gen assembler is now available. The "engine" will fuel Sanger, Illumina, 454, Helicos, and (SOLiD) assemblies for de novo, single and paired read assembly. When using reference sequences, the engine utilizes a unique de novo templated assembly, which sounds like an oxymoron, but the results are fantastic. There are no limits to the number of SNPs per read, providing more accurate assemblies and more accurate signals in transcriptome assemblies.
For the end user, the SNP report is interactive with both the alignment and the strategy view including a depth of coverage histogram, paired end reporting, and automated scaffold creation. SNP reporting includes a wide variety of filtering options to hone in on SNPs of interest. The SNP report will tell you that SNP "A" causes amino acid change "B" in position "C" of CDS/exon "D". Taking things to the protein level is unique. Automated SNP and feature annotation of the consensus from a reference sequence or from NCBI is supported. Assembly results feed directly into ArrayStar for expression analysis including heat maps, scatter plots, and line graphs with heirarchical and K-Means clustering, for those of you performing transcriptome/RNA-Seq work. Assembly results also feed directly to our GenVision genomic mapping software. Primer walking occurs on a genome-wide basis, rather than by individual selection of areas.
DNAStar's first assembler was introduced over 25 years ago, before Apple and Microsoft operating systems were available, and it produced the E. coli genome. We introduced 454 capability two years ago, with a neat trick to handle homopolymeric runs. We encourage any researcher in this field to take our latest assembler for a test drive, as any software mentioned on this site will be playing catch up for a time to come.
For the end user, the SNP report is interactive with both the alignment and the strategy view including a depth of coverage histogram, paired end reporting, and automated scaffold creation. SNP reporting includes a wide variety of filtering options to hone in on SNPs of interest. The SNP report will tell you that SNP "A" causes amino acid change "B" in position "C" of CDS/exon "D". Taking things to the protein level is unique. Automated SNP and feature annotation of the consensus from a reference sequence or from NCBI is supported. Assembly results feed directly into ArrayStar for expression analysis including heat maps, scatter plots, and line graphs with heirarchical and K-Means clustering, for those of you performing transcriptome/RNA-Seq work. Assembly results also feed directly to our GenVision genomic mapping software. Primer walking occurs on a genome-wide basis, rather than by individual selection of areas.
DNAStar's first assembler was introduced over 25 years ago, before Apple and Microsoft operating systems were available, and it produced the E. coli genome. We introduced 454 capability two years ago, with a neat trick to handle homopolymeric runs. We encourage any researcher in this field to take our latest assembler for a test drive, as any software mentioned on this site will be playing catch up for a time to come.
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