most positions are zero depth

[Shawn-X-Zhang]

Ask away!

I use the workflow to analyze nanopore sequencing data of wastewater SARS-CoV-2 samples.
The 'Midnight-ONT/V3' primers were used in amplification. The basecall_model from the fastq files is
[email protected]

The pipeline could not identify a valid basecall model so I over-rided with '[email protected]'.
The pipeline worked without error in the screen.
All samples have zero depth in most positions based on all_depth.txt.

I took five fastq files from wf-artic demo (barcode49, barcode51, etc.) and add them to my sample folder so that they serve as control.
After analysis with the pipeline, my samples still have zero depth in most position.
The demo samples have about 50% percent positions with zero depth.
When I checked the consensus sequences of the demo samples, they are about 29kb, and actually have less than 5% N.
This seems conflict with the depth data.

Should I do some configuration to show maximize the positions with non-zero depth even if the depth is low?
I am also appreciate your suggestion regarding to the choice of basecaller model.

Thanks for creating the pipeline and answer my questions.
Xiangmin

Below is the command used to run the pipeline:
nextflow run epi2me-labs/wf-artic
--fastq 'wf-artic-input/fastq'
--sample_sheet 'wf-artic-input/sample_sheet.csv'
--scheme_name 'SARS-CoV-2'
--scheme_version 'Midnight-ONT/V3'
--override_basecaller_cfg '[email protected]'
-c my_config.cfg
-profile standard