SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
Bioinformatics
; 28(16): 2180-1, 2012 Aug 15.
Article
en En
| MEDLINE
| ID: mdl-22689387
ABSTRACT
UNLABELLED Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling. Analyzing RRBS sequencing data is challenging and specialized alignment/mapping programs are needed. Although such programs have been developed, a comprehensive solution that provides researchers with good quality and analyzable data is still lacking. To address this need, we have developed a Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS) that integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation. AVAILABILITY AND IMPLEMENTATION SAAP-RRBS is freely available to non-commercial users at the web site http//ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
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Análisis de Secuencia de ADN
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Metilación de ADN
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Anotación de Secuencia Molecular
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2012
Tipo del documento:
Article
País de afiliación:
Estados Unidos