need mapping solutions for 454 reads

[eoh001]

Hello
I tried to map 454 reads with GS reference mapper.
I want to map them with different algorithm.
Could you recommed any software good for 454 reads?
Thanks!!!!

[lukas1848]

You could try GMAP or bwa (with sw option set). Do you have PE or SE reads and do you have cDNA or genomic reads?

[ulz_peter]

a very popular algorithm for 454 reads is SSAHA2

[KaiYe]

a newer version of SSAHA2 is SMALT.

[adaptivegenome]

SMALT and BWA-SW are good. We have had some improved results by splitting the reads at homopolymers.