Automatic adapter identification for trimming

[punto_c]

Hello everybody,

I am kind of new ot the analysis of NGS data, so I am sorry if my questions
my be to simple, or not easy to understand

I was wondering if there is any software (or in-house script) that given a rawread automatically selects the adapter sequence
Some software I have used (fastqc) gives information about the overrepresented sequences which could ponteally be adapters to be trimmed

I would really appreciate your suggestions on how to solve this issue

thanks a lot in adavance for your help

Salvo

[Mchicken]

Normally you are aware of your adapter sequences used in the library preparation. As you mentioned Fastqc is also able to check for overrepresented sequences and tells you the possible source like for example ("Illumina Paired End PCR Primer 2").

If you have your adapter sequences you can use for example cutadapt http://code.google.com/p/cutadapt/ which trimms your reads from the adapter contamination.

[GenoMax]

@punto_c: Over-represented sequences should not automatically denote things you would want to trim (adapters etc). If your libraries are well made over-represented sequences, if present, may represent important biology.

Trimmomatic includes adapter sequences for illumina. BBDuk, which is part of BBMap is also easy to use.

[punto_c]

Thank you Mchicken, yes I know my adapters, I am just considering thepossibility to automate the process for an high level software that could be used by clinitians.
So I would like to find a way to automate the trimming

GenoMax thanks a lot I am at the moment comparing some trimming tools, including Trimmomatic. I will also check out BBMap

[Brian Bushnell]

If you have an assembly, and map a bunch of reads using local alignments (so that the trailing mismatching bases are soft-clipped), you could create a consensus of the trailing soft-clipped bases, which would be your adapter sequence. But I don't have or know of any software to automate that; usually I do it manually.