Hello, For Illumina, the Eland tool that comes with the machine is considered pretty good. Other options are MAQ and BWA from Heng Li at The Sanger Institute. Our team is not using BLAT for this purpose.
Hopefully one of these will work out for you, Jennifer Jackson UCSC Genome Bioinformatics Group Rudy Spangler wrote: > Hi guys > > with all the great utilities in the Browser/Tables, are people using it for > aligning short reads (or assembled contigs) from say Illumina sequencing? is > anyone using BLAT for this purpose for example? Im working with about 5 > million single-end reads for a bacterial genome of about 6 MegaBases ... but > highly plastic between strains ... the short reads can be condensed to about > 5 thousand (mostly) non-overlapping contigs ... > > Thanks > > Rudy > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
