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epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
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reference table #79

Closed HannahBenisty closed 8 months ago

HannahBenisty commented 10 months ago

Ask away!

Hi,

I have analyzed my samples using the "minimap2_by_reference" option, specifically for 16S rRNA sequencing. However, I'm uncertain about the specifics of what and how this option measures. Could you provide a detailed description of this option?

Additionally, I would like to know if it's feasible to use this pipeline with FASTQ files generated from PacBio HiFi sequencing, enabling a comparison between the two technologies for the 16S analysis.

Many thanks, Hannah

cjw85 commented 9 months ago

For somewhat obviously reasons we cannot condone the use of this workflow for making comparisons between technologies. 😄

The option you have reference is described in the documentation as:

Add a table with the mean sequencing depth per reference, standard deviation and coefficient of variation. It adds a scatterplot of the sequencing depth vs. the coverage and a heatmap showing the depth per percentile to the report