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Old 05-28-2008, 04:15 PM   #30
JKing
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Location: Wisco

Join Date: May 2008
Posts: 9
Default 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 assemblies or .sqd SeqMan format. Two algorithms ~ de novo or, when references are used, a hybrid algorithm using a combination templated/de novo approach that eliminates the problem of reads getting thrown out even in especially SNPy areas.

The primary viewing and genome completion tool is SeqMan Pro 8, which now includes SNP filtering options to eliminate noise and/or to only annotate reference SNPs of interest. Annotation support provides information like SNP A causes a.a. change B in codon C of CDS/exon D, as well as cross-annotation of the consensus from the reference sequence for use of the consensus in subsequent steps. The other tool for analysis is ArrayStar, which imports transcriptome assemblies for clustering work and traditional heat map, scatter plot, and line graph expression display.

Quick note: I do work for DNAStar as a Next-Gen App. Scientist, but you will find I'm no shill using this site. I actually find this site extremely valuable as a knowledge base for all of us. In this particular thread, however, these products do deserve notice.
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