Hello everyone,
We've implemented a novel tool named skewer for adapter trimming. It is aimed for preprocessing Illumina Paired-end/single-end reads at the moment. The main features are as follows:
* Allow full-length adapter sequence trimming for higher specificity;
* Allow indel errors when finding adapter sequence;
* Very fast: Internally it uses a novel local alignment algorithm that has not been published. In single thread mode, it can process a pair of compressed files, whose uncompressed sizes were about 12G bytes each, in about 30 minutes; it is even faster in multi-thread mode, but the speedup is limited due to the parallelism is only made in the sequence alignment part.
* Quality values aware. It evaluates alignments based on sequence qualities.
* Paired information aware. It is more accurate in case of processing paired-end reads.
If you are interested in using it, please download it from
https://sourceforge.net/projects/skewer/
Any feedback or feature requests are welcome!
We've implemented a novel tool named skewer for adapter trimming. It is aimed for preprocessing Illumina Paired-end/single-end reads at the moment. The main features are as follows:
* Allow full-length adapter sequence trimming for higher specificity;
* Allow indel errors when finding adapter sequence;
* Very fast: Internally it uses a novel local alignment algorithm that has not been published. In single thread mode, it can process a pair of compressed files, whose uncompressed sizes were about 12G bytes each, in about 30 minutes; it is even faster in multi-thread mode, but the speedup is limited due to the parallelism is only made in the sequence alignment part.
* Quality values aware. It evaluates alignments based on sequence qualities.
* Paired information aware. It is more accurate in case of processing paired-end reads.
If you are interested in using it, please download it from
https://sourceforge.net/projects/skewer/
Any feedback or feature requests are welcome!
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