16s rna meta-genomics analysis

Question

[1769mkc]

I have 16s rna meta-genomic sequence data. So far I have done is basecalling using guppy which resulted in fastq files. A total of 96 samples were sequenced.

• I have 96 barcoding folder and inside each folder there are 1962 fastq files.

So do I merge all the fastq reads and make them one file or each file are analysed individually

Few of the pipelines I have read so far for nanopore reads,one of them is this. I would like to assign taxonomic labels to these samples which can be done using kraken or centrifuge. Is it possible to use either of these tools with the above pipeline?

[GenoMax]

NCBI now has 16S/18S/ITS/LSU/SSU pre-formatted blast databases. You could try those out.

[1769mkc]

surely i will use that but right now Im in pre processing step of the data I will find out about the primers and update

[GenoMax]

Are these amplicons done using degenerate primers?

[1769mkc]

I will have to find out what primer we have used

[1769mkc]

No these are not degenerate primers . How to go about it since there are about 1962 fastq files under each barcoding how to go about it. Should I merge all the fastq files and proceed?

[GenoMax]

Since we don't know how these were generated and/or what region you are looking at from 16S you could do the following.

1. If these are distinct sequences then you could align them using blast+ to the database I had suggested above.
2. If they need to be assembled then you could do that next and then align.
3. Take a look at something like this.

[1769mkc]

Actually we started using that epi2me and WIMP when we had less sequence since that happens all in the server side it takes a lot of time then only we started looking how to do locally.

"what region you are looking at from 16S " This I will update