Platform for Drug Discovery

blastn for silva database (SE)


    This pipeline is useful for the researcher who deal with 16s rDNA metagenome data. It will takes a few days to finish whole analysis for the 0.1 million 400 bp single-end data.

    For this pipeline, FASTQ is converted to FASTA, then homology search of blastn is performed against silva SSU database. Using MEGAN software (external standalone tool), output files can be used for taxonomical analysis.

    Input formatFASTQ
    Library layoutSingle-end
    Execution timeAbout a few days for silva

Table of contents


    Raw NGS reads (FASTQ format, Single-end): 1

    • Check the dataset type explanation: this page.


    Execution example1
    1. FASTA file
    FASTQ-FASTA conversion
    2. Blast result
    Result of homology search using blastn


    If you are using this SILVA pipeline, please cite following paper.

    Pruesse, E., C. Quast, K. Knittel, B. Fuchs, W. Ludwig, J. Peplies, and F. O. Glockner (2007) Nuc. Acids Res. Vol. 35, No. 21, p. 7188-7196.
    SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.

Use case

    Example1: Query was Roche454 sequencing data which are comprised of 0.1 million single-end reads with an average length of 400 bp. Blastn homology search against silva SSU database took approximately 4 days.

Related information