ONT MinION QC: Concatenate or Analyze Individually

Question

[Acervo]

Hello everyone!

I am new to handling ONT sequencing data. I am working with a fungus, and the MinION sequencing of its DNA resulted in 80 separate .fastq files (total: 17 GB).

My question concerns the initial Quality Control (QC) step using FastQC. Option A: Should I run FastQC on each of the 80 individual files, or Option B: Should I concatenate (merge) all 80 files into a single .fastq file and run FastQC only once?

Which workflow (A or B) is the most recommended at this point, before the genome assembly stage?"

Answer 1

[GenoMax]

You can concatenate the files and run the QC once.

You should use a QC program meant for long reads such as LongQC (LINK) instead of FastQC (which is meant for short illumina reads). If you have access to the entire run folder then you can also use PycoQC (LINK).

[Acervo]

I got it, thank you so much!! It helped a lot :)