Adapter searching

[seq_GA]

Hi,
We are having Illumina paired end sequenced data with adapters in both 3' and 5' tags.

Is there any open source software to fish for adapters in both 3' (7 bps long) and 5'(6 bps long). Rght now we are using smith-waterman to do local alignment allowing 2 mismatches. Tags are from Illumina sequencing and hence 3' or 5' adapter cab be found in eirther read1 or read2 of Illumina paired end sequnced data.

The whole process is very slow because of smith-waterman.

I am looking for a tool which can look for both 3' and 5' adapter allowing 2 mismatches in the adapter.

Thanks.

[gaffa]

Here are some alternatives, some of these can probably do the job: http://biostar.stackexchange.com/que...ation-illumina

[BAMseek]

Hi seq_GA,

Some of the trimming algorithms use Hamming distance (only looking at mismatches and not indels). These would probably be faster than a Smith-Waterman since the search space is smaller.

For methods that accommodate indels, you might try Btrim: it uses an optimized Smith-Waterman implementation using bit-level parallelism. I haven't tried the program myself (only available on Linux and no source code), but I think it is an interesting approach.

Justin

[NicoBxl]

cutadapt is pretty good too : http://code.google.com/p/cutadapt/