Probabilistic base calling of Solexa sequencing data.
BMC Bioinformatics
; 9: 431, 2008 Oct 13.
Article
em En
| MEDLINE
| ID: mdl-18851737
ABSTRACT
BACKGROUND:
Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology.RESULTS:
We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads.CONCLUSION:
We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
DNA Viral
/
Análise de Sequência de DNA
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2008
Tipo de documento:
Article
País de afiliação:
Suíça