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Fig. 1 | BMC Bioinformatics

Fig. 1

From: 16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing

Fig. 1

Flow chart of the 16SPIP analysis pipeline. During the pre-processing stage, 16S metagenomic raw data can either be used directly or subjected to file format conversion. The data were subjected to the removal of adapter, low-quality, and low-complexity sequences. The paired-end reads can either be merged using PEAR or used directly. In fast mode, pathogen identification was achieved by alignment against the 16S pathogen database using the BWA-MEM algorithm. In sensitive mode, the BWA-MEM algorithm was used for alignment against the 16S full-length database. Sequence reads with greater than 99% similarity to the reference sequence were extracted and re-aligned against the 16S full-length database using BLASTN. The test report generated from 16SPIP includes the basic information for the sample, pathogen detection results, and distribution of bacterial species

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BMC Bioinformatics

ISSN: 1471-2105

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