This is why @wytamma.bsky.social and I have been writing SNIPPY-NG ! It will support short reads, long reads, and assemblies as inputs. You can check it out at github.com/centre-patho...

It's not ready for prime-time yet, but it's useable!

Slightly out of context but snippy too is a great variant calling tool.. @torstenseemann.bsky.social could add support for long reads? 😄

github.com/tseemann/sni...

This should help with the -x flag…

github.com/barricklab/b...

Amazing tool. Any plans to release a singularity or docker container of this. Will be of massive help..

Found this resource www.tandfonline.com/doi/full/10....

Sorry meant 0.1%. A lot of tinkering at db level might be needed before the illumina v4-v5 could be analysed.

Would it make sense to create otu bins till 99% at 1% increments and gather a representative sequence? The repset could be made into a strain blast db or bowtie index. No. Of mapped reads to strain db divided by total reads should give strain level relative abundance from v4 regions.

Full length 16S data is from Sanger seq or extracted from wgs denovo assembly?

Welcome to #bluesky team CEH shoutout to Tim from India this time!

Keeping it behind a landing page with necessary forms and authentication is also reasonable as long as wait times are not too long imho.

There is no problem in wanting to know how many times and by whom data has been accessed. But if no personal identity info is part of the data then i see no reason why in the age of figshare, sra and other open repos intent to share is hiding behind this tactic.

Data not shared = science didnt happen.

Journals should do a test request and then send notice why such papers shouldn’t be retracted.

If bclconvert is done then output of that too passed to multiqc for a detailed summary