Demultiplexing MinION reads

Question

[jeccy.J]

Hi Community,

I have run Guppy on naopore reads for the basecalling and generated a final merged fastq file. Next, for demultiplexing I have seen a couple of option available, such as Porechop, Last and qcat. Can anyone suggest me from their earlier experience which tool I should use for demultiplexing of the basecalled fastq reads? As an input data i have the a .fastq file and one fasta file with all the barcode.

JC

Answer 1

[shelkmike]

I use Porechop and I have no problems with it.

[jeccy.J]

Could you please let me know the running command. I checked the manual it looks like : porechop -i input_reads.fastq.gz -b output_dir here, how i should provide my input barcode fasta file?

[GenoMax]

https://github.com/rrwick/Porechop#barcode-demultiplexing

Scroll down at the link above. Looks like you need to edit adapters.py script and add them if you use custom barcodes.

[jeccy.J]

Do you use Guppy for basecalling or any other tool?

[shelkmike]

Sorry, I didn't notice your first comment. You should manually edit the adapters.py file to add barcodes. I use guppy for basecalling and then porechop for demultiplexing or trimming when non-standard adapters are used.

Answer 2

[colindaven]

I think the generally accepted and most up to date tool to use is

guppy_barcoder

from ONT

Usage is quite easy (it runs on fastq files output by guppy, not on FAST5 files).