looking for 16S RNA sequence consensus

Question

[sacha]

I m looking for a 16s RNA sequence consensus ? Does it exist ? I want to make some alignement, to know exactly where my read comes from . Does my read comes from V3 or V4 region more precisely.

[sacha]

What about the fasta sequence ?

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts/comments. SUBMIT ANSWERS is only for NEW answers to original question.

[GenoMax]

What fasta sequence do you want?

[sacha]

I m looking for a 16S RNA fasta sequence. My objectif is to align a fastq on this reference using bwa.

[GenoMax]

Are you interested in a specific bacterium? As linked below SILVA database has this file (or use one of the other db) which will have many organisms so you can select the sequence that you want from that file.

If you are looking to classify a metagenomic dataset then Kraken or Kaiju would be better options.

Answer 1

[shenwei356]

• NCBI blastdb: ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz
• Silva: https://www.arb-silva.de/download/arb-files/
• Greengenes: http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/

Answer 2

[sacha]

Same question there Where Do I Find The 16S Rdna Reference Sequences (Metagenomics)