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Old 06-15-2008, 06:34 AM   #1
JKing
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Default SeqMan NGen

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.
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Old 06-15-2008, 06:42 AM   #2
JKing
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Default SeqMan NGen

One other thing, SeqMan NGen does not just "report" large insertions, deletions, and relocations. Instead, it directly assembles them, whether you have paired end reads or not. Most software requires paired ends to simply identify such regions, but SeqMan NGen will directly assemble them into so-called "SuperContigs" regardless of paired end data.
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Old 06-15-2008, 07:46 AM   #3
ECO
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Hey JKing! Sounds great! Glad to see you're supporting SOLiD!

My first run ends Wednesday so I will be interested in looking at a trial version soon!
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Old 06-17-2008, 01:06 PM   #4
bioinfosm
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Is there a link from where to get/request the trial version?

Thanks...
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Old 06-17-2008, 01:12 PM   #5
JKing
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Default NGen demos

The IT group is working up the infrastructure on our website for direct demo requests, and that should be up soon. In the meantime, just email [email protected] and we'll set you up.
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Old 10-17-2008, 06:10 AM   #6
Blaize
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Is there any experience, benchmarking result of NGen?
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Old 10-17-2008, 10:19 AM   #7
JKing
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Here is the link to SeqMan NGen free trials: http://www.dnastar.com/forms/demo_request.php

As for benchmarks, that is a fairly loaded question as there is such a wide variety of assembly approaches. Please feel free to email [email protected], and we can discuss your particular project.
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