Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 May 10:17:208.
doi: 10.1186/s12859-016-1069-7.

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

Marc Sturm  1 , Christopher Schroeder  2 , Peter Bauer  2
Affiliations

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

Marc Sturm et al. BMC Bioinformatics. .

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Read layout with adapter contamination (a) and insert match algorithm examples with different offsets (b). Inserts are colored grey, adapter remains are colored black. Reverse reads are displayed with reverse-complementary sequence to facilitate visual comparison of sequences
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Bolger AM, et al. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. doi: 10.1093/bioinformatics/btu170. - DOI - PMC - PubMed
    1. Dodt M, et al. FLEXBAR - Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology. 2012;1:895–905. doi: 10.3390/biology1030895. - DOI - PMC - PubMed
    1. Garrison E, et al. Haplotype-based variant detection from short-read sequencing. 2012. http://arxiv.org/abs/1207.3907. Accessed 18 Jan 2016.
    1. Giorgi FM, et al. An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis. PLoS ONE. 2013;8(12):e85024. doi: 10.1371/journal.pone.0085024. - DOI - PMC - PubMed
    1. Jiang H, et al. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014;15:182. doi: 10.1186/1471-2105-15-182. - DOI - PMC - PubMed