TagDust—a program to eliminate artifacts from next generation sequencing data

Motivation: Next-generation parallel sequencing technologies produce large quantities of short sequence reads. Due to experimental procedures various types of artifacts are commonly sequenced alongside the targeted RNA or DNA sequences. Identification of such artifacts is important during the develo...

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Detalles Bibliográficos
Autores principales: Lassmann, Timo, Hayashizaki, Yoshihide, Daub, Carsten O.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781754/
https://www.ncbi.nlm.nih.gov/pubmed/19737799
http://dx.doi.org/10.1093/bioinformatics/btp527
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author Lassmann, Timo
Hayashizaki, Yoshihide
Daub, Carsten O.
author_facet Lassmann, Timo
Hayashizaki, Yoshihide
Daub, Carsten O.
author_sort Lassmann, Timo
collection PubMed
description Motivation: Next-generation parallel sequencing technologies produce large quantities of short sequence reads. Due to experimental procedures various types of artifacts are commonly sequenced alongside the targeted RNA or DNA sequences. Identification of such artifacts is important during the development of novel sequencing assays and for the downstream analysis of the sequenced libraries. Results: Here we present TagDust, a program identifying artifactual sequences in large sequencing runs. Given a user-defined cutoff for the false discovery rate, TagDust identifies all reads explainable by combinations and partial matches to known sequences used during library preparation. We demonstrate the quality of our method on sequencing runs performed on Illumina's Genome Analyzer platform. Availability: Executables and documentation are available from http://genome.gsc.riken.jp/osc/english/software/. Contact: timolassmann@gmail.com
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spelling pubmed-27817542009-11-25 TagDust—a program to eliminate artifacts from next generation sequencing data Lassmann, Timo Hayashizaki, Yoshihide Daub, Carsten O. Bioinformatics Applications Note Motivation: Next-generation parallel sequencing technologies produce large quantities of short sequence reads. Due to experimental procedures various types of artifacts are commonly sequenced alongside the targeted RNA or DNA sequences. Identification of such artifacts is important during the development of novel sequencing assays and for the downstream analysis of the sequenced libraries. Results: Here we present TagDust, a program identifying artifactual sequences in large sequencing runs. Given a user-defined cutoff for the false discovery rate, TagDust identifies all reads explainable by combinations and partial matches to known sequences used during library preparation. We demonstrate the quality of our method on sequencing runs performed on Illumina's Genome Analyzer platform. Availability: Executables and documentation are available from http://genome.gsc.riken.jp/osc/english/software/. Contact: timolassmann@gmail.com Oxford University Press 2009-11-01 2009-09-07 /pmc/articles/PMC2781754/ /pubmed/19737799 http://dx.doi.org/10.1093/bioinformatics/btp527 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Lassmann, Timo
Hayashizaki, Yoshihide
Daub, Carsten O.
TagDust—a program to eliminate artifacts from next generation sequencing data
title TagDust—a program to eliminate artifacts from next generation sequencing data
title_full TagDust—a program to eliminate artifacts from next generation sequencing data
title_fullStr TagDust—a program to eliminate artifacts from next generation sequencing data
title_full_unstemmed TagDust—a program to eliminate artifacts from next generation sequencing data
title_short TagDust—a program to eliminate artifacts from next generation sequencing data
title_sort tagdust—a program to eliminate artifacts from next generation sequencing data
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781754/
https://www.ncbi.nlm.nih.gov/pubmed/19737799
http://dx.doi.org/10.1093/bioinformatics/btp527
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