AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads

Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. Based on the decomposition of specified alien nucleotide sequences into k-mers, AlienTrimme...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Vol. 102; no. 5-6; pp. 500 - 506
Main Authors: Criscuolo, Alexis, Brisse, Sylvain
Format: Journal Article
Language:English
Published: United States Elsevier Inc 01.11.2013
Subjects:
Adapter oligonucleotides
Algorithms
Base Sequence
Computational Biology
DNA
DNA - genetics
DNA Contamination
DNA Primers
genetics
high-throughput nucleotide sequencing
High-Throughput Nucleotide Sequencing - methods
High-throughput sequencing
k-mer decomposition
methods
nucleotide sequences
Polynomial algorithm
Quality Control
Raw read trimming
Sequence Analysis, DNA
Sequence Analysis, DNA - methods
Short contaminant sequence
Software
Raw read trimming
Adapter oligonucleotides
High-throughput sequencing
Short contaminant sequence
Polynomial algorithm
k-mer decomposition
ISSN:0888-7543, 1089-8646, 1089-8646
Online Access:Get full text
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Summary:Contaminant oligonucleotide sequences such as primers and adapters can occur in both ends of high-throughput sequencing (HTS) reads. AlienTrimmer was developed in order to detect and remove such contaminants. Based on the decomposition of specified alien nucleotide sequences into k-mers, AlienTrimmer is able to determine whether such alien k-mers are occurring in one or in both read ends by using a simple polynomial algorithm. Therefore, AlienTrimmer can process typical HTS single- or paired-end files with millions of reads in several minutes with very low computer resources. Based on the analysis of both simulated and real-case Illumina®, 454™ and Ion Torrent™ read data, we show that AlienTrimmer performs with excellent accuracy and speed in comparison with other trimming tools. The program is freely available at ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/. •Removal of alien sequences (adapters, primers) from raw reads improves the quality of results from downstream analyses.•AlienTrimmer allows detecting and removing multiple alien sequences in both ends of sequence reads.•AlienTrimmer performs accurately and has fast running time.
Bibliography:http://dx.doi.org/10.1016/j.ygeno.2013.07.011
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ISSN:0888-7543
1089-8646
1089-8646
DOI:10.1016/j.ygeno.2013.07.011