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Old 02-04-2008, 07:22 AM   #5
lh3
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Location: Boston

Join Date: Feb 2008
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Thank you very much for the awesome post! Just a few comments.

1. In a commercial package, NCGR uses GMAP (http://www.gene.com/share/gmap/) to alignment Solexa reads. GMAP is free, though.

2. Synamatix has SXOligoSearch (http://synasite.mgrc.com.my:8080/sxo...ligoSearch.php). It is commercial and from the online decription it looks very promising.

3. SOAP (http://soap.genomics.org.cn) by Ruiqiang Li, as has been pointed by ECO.

4. Maq is also able to find SNPs with its own alignment. It has a graphical viewer, but again for its own alignment format.

5. Illumina has a software list: http://www.illumina.com/pagesnrn.ilmn?ID=245. But most of the listed softwares have been quoted here. :-)

6. Anthony Fejes discussed some softwares in his blog (http://www.fejes.ca/labels/DNA.html). May be helpful to someone, too.

7. SSAHA has been optimized for short-reads, too. But yes, SSAHASNP appears in your "SNP/INDEL discovery" category.

8. Ladeana from Gabor's group has recently published a paper on Nature Methods, using their MASAIC and PolyBayesShort.

Last edited by lh3; 02-04-2008 at 07:34 AM.
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