Genome assembly tools

Question

[Clarancia]

My objective is to mine SSR from the genome sequences. But all i have is only scaffolds and contigs data about the organisms. Please suggest whether it is correct to mine ssr at the scafold and contig level. If not, suggest some tools to align these scafolds and contigs to higher assembly level to perform further analysis.

[h.mon]

Did you search the forum (e.g., have you read this post)?

What SSR has to do with genome assembly tools?

P.S.: and please, please, please, to not link to that crappy, advertisement-bloated site. Link to a paper or WikiPedia, in case you think people here do not know what SSR is.

[Michael]

Sorry, that link was me... I didn't see most of the adds probably due to add block, now linking to Wikipedia disambiguation.

Answer 1

[Michael]

The most common tool to search for repeats is repeatmasker, it can be run on contigs and scaffolds as well.

Answer 2

[Prasad]

have you tried misa (well cited) with the primer designing scripts. other tools like SSRIT, Poly, GMATO