non paired adapters in 454 data

[donniemarco]

Can anyone please let me know any preprocessing steps (like cleansing adapters or any other steps) for non paired 454 sequenced data and any available tool that allows the same, before assembling is performed.
Thanks

[sklages]

This all depends heavily on what kind of library (ESTs, gen. shotgun, fosmid pool etc) you are using. This decides if you have any kind of vector and/or adaptors to be removed. If your library is free of any unwanted sequence and you don't see the need for screening before assembly, then fine, go for it.

If not, tools like SSAHA (Sanger Centre), cross_match (WashU), megablast (NCBI) might be of assistance. There are many more.

Some assemblers also provide some kind of clipping functionality (e.g. MIRA).

cheers,
Sven

[donniemarco]

Thanks for your reply. It was really helpful.

What about PolyA and PolyT sequences? How long any sub-sequence be to qualify as polyA or polyT.

[sklages]

Depends on your type of library and on the quality of the reads. Give it a try, play around.

Sven