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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