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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

Fig. 2

Summary of the analytical capability of the bioinformatics pipeline. Data can currently be preprocessed by two tools, Columbia University’s Preprocessing Procedure (CUPP) or a taxonomy analysis based on NCBI taxonomy results. Then, reads retained after the pre-processing manipulations are assembled de novo. Nearest neighbors and SNP profiling then occurs by comparing the identified contigs to NCBI databases. A reference map is created, and the SNP profile from those mapping results provides a comprehensive comparison of the taxonomical near neighbors. Finally, all the unmapped reads are extracted and used as input to the next iteration

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