NCBI BLAST+ integrated into Galaxy

GigaScience

Nicola Soranzo²  James E. Johnson¹  Björn Grüning⁴  John M. Chilton¹  Peter J. A. Cock³ 

[1] Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant St. SE, Minneapolis, 55455, MN, USA;CRS4, Loc. Piscina Manna, Pula, 09010, CA, Italy;Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK;Department of Computer Science, Albert-Ludwigs-University of Freiburg, Georges-Köhler-Allee 106, Freiburg 79110, Germany

关键词: Sequence analysis;    Annotation;    Reproducibility;    Workflow;    Accessibility;    Pipeline;    BLAST;    Galaxy;   

Others  :  1223626
DOI  :  10.1186/s13742-015-0080-7

 received in 2014-12-31, accepted in 2015-08-18,  发布年份 2015

【 摘 要 】

Background

The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows.

Findings

The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible.

Conclusions

This project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.

【 授权许可】

   
2015 Cock et al.

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