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.
|Execution time||About a few days for silva|
Table of contents
- Check the dataset type explanation: this page.
Raw NGS reads (FASTQ format, Single-end): 1
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.
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.