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Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline

Joachim De Schrijver UGent, KIM DE LEENEER UGent, Steve Lefever UGent, Nick Sabbe UGent, Filip Pattyn UGent, Filip Van Nieuwerburgh UGent, Paul Coucke UGent, Dieter Deforce UGent, Jo Vandesompele UGent and Sofie Bekaert UGent, et al. (2010) BMC BIOINFORMATICS. 11.
abstract
Background: Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions. Results: We developed an integrated database oriented software pipeline for analysis of 454/Roche GS-FLX amplicon resequencing experiments using Perl and a relational database. The pipeline enables variation detection, variation detection validation, and advanced data analysis, which provides information that can be used to optimize PCR efficiency using traditional means. The modular approach enables customization of the pipeline where needed and allows researchers to adopt their analysis pipeline to their experiments. Clear documentation and training data is available to test and validate the pipeline prior to using it on real sequencing data. Conclusions: We designed an open-source database oriented pipeline that enables advanced analysis of 454/ Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is also a set of standard reporting scripts available.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
GENOME, ALIGNMENT
journal title
BMC BIOINFORMATICS
BMC Bioinformatics
volume
11
article_number
269
pages
12 pages
Web of Science type
Article
Web of Science id
000278362700002
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
3.028 (2010)
JCR rank
4/35 (2010)
JCR quartile
1 (2010)
ISSN
1471-2105
DOI
10.1186/1471-2105-11-269
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
815939
handle
http://hdl.handle.net/1854/LU-815939
date created
2009-12-23 12:09:47
date last changed
2012-11-06 11:54:24
@article{815939,
  abstract     = {Background: Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR reactions.
Results: We developed an integrated database oriented software pipeline for analysis of 454/Roche GS-FLX amplicon resequencing experiments using Perl and a relational database. The pipeline enables variation detection, variation detection validation, and advanced data analysis, which provides information that can be used to optimize PCR efficiency using traditional means. The modular approach enables customization of the pipeline where needed and allows researchers to adopt their analysis pipeline to their experiments. Clear documentation and training data is available to test and validate the pipeline prior to using it on real sequencing data.
Conclusions: We designed an open-source database oriented pipeline that enables advanced analysis of 454/ Roche GS-FLX amplicon resequencing experiments using SQL-statements. This modular database approach allows easy coupling with other pipeline modules such as variant interpretation or a LIMS system. There is also a set of standard reporting scripts available.},
  articleno    = {269},
  author       = {De Schrijver, Joachim and DE LEENEER, KIM and Lefever, Steve and Sabbe, Nick and Pattyn, Filip and Van Nieuwerburgh, Filip and Coucke, Paul and Deforce, Dieter and Vandesompele, Jo and Bekaert, Sofie and HELLEMANS, JAN and Van Criekinge, Wim},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keyword      = {GENOME,ALIGNMENT},
  language     = {eng},
  pages        = {12},
  title        = {Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline},
  url          = {http://dx.doi.org/10.1186/1471-2105-11-269},
  volume       = {11},
  year         = {2010},
}

Chicago
De Schrijver, Joachim, Kim De Leeneer, Steve Lefever, Nick Sabbe, Filip Pattyn, Filip Van Nieuwerburgh, Paul Coucke, et al. 2010. “Analysing 454 Amplicon Resequencing Experiments Using the Modular and Database Oriented Variant Identification Pipeline.” Bmc Bioinformatics 11.
APA
De Schrijver, Joachim, De Leeneer, K., Lefever, S., Sabbe, N., Pattyn, F., Van Nieuwerburgh, F., Coucke, P., et al. (2010). Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. BMC BIOINFORMATICS, 11.
Vancouver
1.
De Schrijver J, De Leeneer K, Lefever S, Sabbe N, Pattyn F, Van Nieuwerburgh F, et al. Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. BMC BIOINFORMATICS. 2010;11.
MLA
De Schrijver, Joachim, Kim De Leeneer, Steve Lefever, et al. “Analysing 454 Amplicon Resequencing Experiments Using the Modular and Database Oriented Variant Identification Pipeline.” BMC BIOINFORMATICS 11 (2010): n. pag. Print.