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Hi Everyone,
I have recently acquired 454 amplicon sequences. It is vital that I use a alignment method that does not depend on breaking the reads into smaller ones like BWA. I want to use a program that will align long reads to the reference and also perform variant calling. I am in the process of using 454 gsAmplicon for the alignment and wanted to ask if there are other good softwares for 454 amplicon long read alignment.
I have recently acquired 454 amplicon sequences. It is vital that I use a alignment method that does not depend on breaking the reads into smaller ones like BWA. I want to use a program that will align long reads to the reference and also perform variant calling. I am in the process of using 454 gsAmplicon for the alignment and wanted to ask if there are other good softwares for 454 amplicon long read alignment.