Institut Pasteur, Genotyping of Pathogens and Public Health Platform (PF8), 28 rue du Dr Roux, 75724 Paris Cedex, France; Institut Pasteur, Microbial Evolutionary Genomics Unit, 28 rue du Dr Roux, 75724 Paris Cedex, France; CNRS, UMR3525, 75015 Paris, France.
Institut Pasteur, Genotyping of Pathogens and Public Health Platform (PF8), 28 rue du Dr Roux, 75724 Paris Cedex, France; Institut Pasteur, Microbial Evolutionary Genomics Unit, 28 rue du Dr Roux, 75724 Paris Cedex, France; CNRS, UMR3525, 75015 Paris, France.
Genomics. 2013 Nov-Dec;102(5-6):500-6. doi: 10.1016/j.ygeno.2013.07.011. Epub 2013 Aug 1.
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/.
污染物寡核苷酸序列，如引物和接头，可能出现在高通量测序（HTS）读取的两端。为了检测和去除这些污染物，开发了 AlienTrimmer。基于将指定的外来核苷酸序列分解成 k-mers，AlienTrimmer 能够通过使用简单的多项式算法来确定这些外来 k-mers 是否出现在一个或两个读取端。因此，AlienTrimmer 可以在几分钟内处理典型的 HTS 单端或双端文件，使用非常低的计算机资源处理数百万个读取。基于对模拟和真实案例的 Illumina®、454™ 和 Ion Torrent™ 读取数据的分析，我们表明与其他修剪工具相比，AlienTrimmer 在准确性和速度方面表现出色。该程序可在 ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/ 上免费获得。
