AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
Identifieur interne : 000B04 ( Ncbi/Merge ); 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
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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><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23912058</PMID><DateCompleted><Year>2014</Year><Month>07</Month><Day>18</Day></DateCompleted><DateRevised><Year>2013</Year><Month>12</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8646</ISSN><JournalIssue CitedMedium="Internet"><Volume>102</Volume><Issue>5-6</Issue><PubDate><MedlineDate>2013 Nov-Dec</MedlineDate></PubDate></JournalIssue><Title>Genomics</Title><ISOAbbreviation>Genomics</ISOAbbreviation></Journal><ArticleTitle>AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.</ArticleTitle><Pagination><MedlinePgn>500-6</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ygeno.2013.07.011</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0888-7543(13)00148-1</ELocationID><Abstract><AbstractText>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. 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