Introduction

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 a higher sensitivity. The number of remaining adapter bases after trimming is reduced by up to 90 %, depending on the compared tool. In simulations with different error rates, we found that SeqPurge is also the most error-tolerant adapter trimmer in the comparison.SeqPurge achieves a very high sensitivity and a high error-tolerance, combined with a specificity and runtime that are comparable to other state-of-the-art adapter trimmers. The very good adapter trimming performance, complemented with additional features such as quality-based trimming and basic quality control, makes SeqPurge an excellent choice for the pre-processing of paired-end NGS data.

Publications

  1. SeqPurge: highly-sensitive adapter trimming for paired-end NGS data.
    Cite this
    Sturm M, Schroeder C, Bauer P, 2016-05-01 - BMC bioinformatics

Credits

  1. Marc Sturm
    Developer

    Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Germany

  2. Christopher Schroeder
    Developer

    Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Germany

  3. Peter Bauer
    Investigator

    Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Germany

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT000097
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByPeter Bauer