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Old 05-29-2008, 05:38 PM   #32
JKing
Junior Member
 
Location: Wisco

Join Date: May 2008
Posts: 9
Default 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 in depth information on SeqMan Genome Assembler (SGA), or to perform assemblies with their data, is to email info@dnastar.com. Like I said, I'm not here to hawk a product, but to continue to develop my own knowledge. Plus, posting technical specifics on a public forum runs the risk that the information will linger here and be old in a month when a new SGA version is released. Since you asked, however:

Have you done any work with SOLiD data?
SGA does accept and assemble csfasta files, and some of its specific trimming options for this data overcome some of the problems inherent in colorspace fasta files.

Any comments on how it runs assemblies on standalone desktop-y caliber machines?
SGA runs on 64 bit operating systems to eliminate any limits on RAM. For short read assemblies, it requires a computer with augmented (but not massively so) RAM. SGA is simply a command line assembler which provides .ace or .sqd output. All of the SNP filtering and codon analysis, as well as expression analysis, occurs in SeqMan Pro of the Lasergene suite and in ArrayStar, respectively (or in other software that accepts .ace files). The end user therefore does not require anything special computer-wise to perform the post-assembly analyses.
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