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Question: Demultiplexing MinION reads
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gravatar for jeccy.J
6 weeks ago by
jeccy.J • 50
Argentina
jeccy.J • 50 wrote:

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
demutiplex • 141 views
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modified 6 weeks ago by shelkmike • 380 • written 6 weeks ago by jeccy.J • 50
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gravatar for shelkmike
6 weeks ago by
shelkmike • 380
Russian Federation
shelkmike • 380 wrote:

I use Porechop and I have no problems with it.
ADD COMMENT • link written 6 weeks ago by shelkmike • 380

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?

ADD REPLY • link written 6 weeks ago by jeccy.J • 50

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.

ADD REPLY • link modified 6 weeks ago • written 6 weeks ago by GenoMax ♦ 96k

Do you use Guppy for basecalling or any other tool?

ADD REPLY • link written 4 weeks ago by jeccy.J • 50

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.

ADD REPLY • link written 4 weeks ago by shelkmike • 380
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