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Forum: Bioinformatics 11-21-2008, 07:25 AM
Replies: 236
Views: 510,756
Posted By JKing
You're right...

Agreed, I was too simplistic in my critique of MAQ for a next-generation sequencing board. Aligners can exceed 2 mismatches in certain situations, but in general the rule is that >2 mismatches lead...
Forum: Bioinformatics 11-20-2008, 05:59 PM
Replies: 236
Views: 510,756
Posted By JKing
SeqMan NGen

Update: I visit this site quite a bit to understand the tools available and where this technology is taking us, but I haven't actually posted in some time. Here's an update if you are interested in...
Forum: Bioinformatics 10-17-2008, 11:19 AM
Replies: 6
Views: 4,404
Posted By JKing
Here is the link to SeqMan NGen free trials: ...

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...
Forum: Bioinformatics 06-17-2008, 02:12 PM
Replies: 6
Views: 4,404
Posted By JKing
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.
Forum: Bioinformatics 06-15-2008, 12:53 PM
Replies: 23
Views: 6,909
Posted By JKing
The SeqMan NGen effectively trims these adapters...

The SeqMan NGen effectively trims these adapters and assembles the resulting reads. This is true for small RNA or any target validation run. It's worth a look.
Forum: Bioinformatics 06-15-2008, 07:42 AM
Replies: 6
Views: 4,404
Posted By JKing
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...
Forum: Bioinformatics 06-15-2008, 07:34 AM
Replies: 6
Views: 4,404
Posted By JKing
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...
Forum: Bioinformatics 05-29-2008, 05:38 PM
Replies: 236
Views: 510,756
Posted By JKing
Nice to meet you, Eco

Thanks for the warm welcome, Eco. This site is poised to be a valuable base of knowledge for all of us who are highly interested in this technology.

The best way for visitors of this site to get...
Forum: Bioinformatics 05-28-2008, 05:15 PM
Replies: 236
Views: 510,756
Posted By JKing
Sga

Another couple of tools:

SeqMan Genome Assembler -- an assembler (as opposed to a templated read aligner) of Illumina, 454, and/or Sanger single read and paired end data. Output as .ace...
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