Trimming of adapter sequences from short read data is a common preprocessing step during NGS data analysis. When performing paired-end sequencing, the overlap between forward and reverse read can be used to identify excess adapter sequences. This is exploited by several previously published adapter trimming tools. However, our evaluation on amplicon-based data shows that most of the current tools are not able to remove all adapter sequences and that adapter contamination may even lead to spurious variant calls.
Here we present SeqPurge ( https://github.com/imgag/ngs-bits ), a highly-sensitive adapter trimmer that uses a probabilistic approach to detect the overlap between forward and reverse reads of Illumina sequencing data. SeqPurge can detect very short adapter sequences, even if only one base long. Compared to other adapter trimmers specifically designed for paired-end data, we found that SeqPurge achieves...

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

10.1186/s12859-016-1069-7