AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
Identifieur interne : 000B04 ( Ncbi/Checkpoint ); précédent : 000B03; suivant : 000B05AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
Auteurs : Alexis Criscuolo [France] ; Sylvain Brisse [France]Source :
- Genomics [ 1089-8646 ]
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA.
- Algorithms, Base Sequence, Computational Biology, DNA Contamination, DNA Primers, Quality Control, Software.
Abstract
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/.
DOI: 10.1016/j.ygeno.2013.07.011
PubMed: 23912058
Affiliations:
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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/.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Île-de-France</li></region><settlement><li>Paris</li></settlement></list><tree><country name="France"><region name="Île-de-France"><name sortKey="Criscuolo, Alexis" sort="Criscuolo, Alexis" uniqKey="Criscuolo A" first="Alexis" last="Criscuolo">Alexis Criscuolo</name></region><name sortKey="Brisse, Sylvain" sort="Brisse, Sylvain" uniqKey="Brisse S" first="Sylvain" last="Brisse">Sylvain Brisse</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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