blastn for silva database (SE)

Introduction

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 format	FASTQ
Library layout	Single-end
Execution time	About a few days for silva

Table of contents

• blastn for silva database (SE)
  • Introduction
  • Table of contents
  • Inputs
  • Outputs
  • Comments
  • Use case
  • Related information

Inputs

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

• Check the dataset type explanation: this page.

Outputs

Execution example1



1. FASTA file FASTQ-FASTA conversion

2. Blast result Result of homology search using blastn

Comments

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

Public


BLAST	(Original site)
MEGAN	(Original site)
SILVA	(Original site)