Ezra Herman

Hi Jacob, it is my understanding that in the past, the `colors` argument changed the colour of the line only. It now changes the colour of the line and the...

Best practice for ONT metagenomics

11

I am in the process of determining whether sourmash is the right tool for my metagenomic analyses. I am mostly using ONT data at the moment. Similar to previous posts...

`sig describe` error when subdirectory name contains "sourmash"

2

Hi, I have found that `sourmash sig describe` returns an error if the signature file is located in a subdirectory that contains the string "sourmash". I am running sourmash version...

Reducing the proportion of unclassified reads (dorado versions and trimming options)

3

I am sequencing barcoded samples on a MinION and performing basecalling and demultiplexing using dorado server in MinKNOW, with barcode trimming and mid-read barcode filtering enabled. Approximately 25% of reads...

Change in Snakemake rerun behaviour

2

As outlined in [this post](https://github.com/snakemake/snakemake/issues/1694) and the snakemake manual under `--rerun-triggers`, snakemake >=7.8 now reruns by default after changes in code, parameter values, input files and software environments, in addition...

Importing a Python module within a Snakemake module raises a `ModuleNotFoundError`

2

**Snakemake version** 8.14.0 **Describe the bug** When a Snakemake module imports its Python module, a `ModuleNotFoundError` is raised. However, when the module is executed on its own, no such error...

I understand from this 2019 issue (#353) that minimap2 ignores base qualities. However the man page lists the `-Q` option: "Ignore base quality in the input file." Does minimap2 consider...

Variation in relative abundances of simulated Zymo mock microbes

1

Hi, We've been trying to simulate Zymo mock communities using your "even" pre-trained model. We've consistently found *Staphylococcus aureus* to be seemingly undersimulated, while *Cryptococcus neoformans* appears to be oversimulated....

# Issue Report ## Please describe the issue: I am getting in touch to ask for details on Dorado's barcode trimming efficiency. In some of my samples I have found...

Mismatch in read quality between input and simulated reads

2

Hi, We have been using NanoSim v3.2.3, and comparing the read qualities in input and simulated reads. ## Input We are characterising on approx 300k reads with the following quality...