Removing homopolymer associated indels from EST assembly

[JackieBadger]

Hi,

Can anyone tell me if they know of a way to batch ignore indels associated with homopolymer runs of a specified length?

I performed my de novo assemblies in Mira3, and am not sure if there is a way to perform this during the assembly.

Any help would be greatly appreciated.

Cheers,

Jack

[SES]

It may be a better solution to deal with homopolymers before you do the assembly. That is, quality trim/filter your reads, then do the assembly and homopolymers should be less of an issue.