Frequently Asked Questions - chill-filter

Please check out the User Guide!!

And, if you have a question that's not answered below, ask it in the issue tracker!

When I upload my sample, what is being uploaded?!

A k-mer summary (or sketch) of your sample is calculated locally, and then uploaded to the chill-filter Web site. This summary is typically under a megabyte in size, even for large shotgun data sets; you can download it from the chill-filter site if you want to see the actual size.

To calculate the sketch locally, chill-filter uses in-browser k-mer sketching, provided by the branchwater project.

This means that chill-filter doesn't "see" your reads, or the complete data set; it only has access to the sketch. And you can delete your sketch at any time.

For more information on sketching, as well as an over-abundance of technical details, please see the sourmash documentation.

How can I see which specific microbial or plant genomes are in my sample?

You can see matches to specific plant genomes, but not to specific microbial genomes. You will be able to, eventually! But for now, you'll have follow up on our sequence composition report yourself.

What happens with overlaps between matches?

If sequence is shared between two matches, it will be assigned uniquely to the first match in the list. This is known as "greedy assignment" and is part of the sourmash gather algorithm.

What if there's contamination in the database?

We're 100% reliant on the genomes in the reference database, so the match that's displayed is to the contents of the genome record. If the genome record is contaminated, then that will be part of the match statistics.

That having been said, if the contamination is something that is shared between multiple genomes in the reference collection, the match will be assigned to the largest match - which often will be the source of the contamination, not the contaminated genome. See the question above about overlaps!

I've downloaded a CSV results file; how do I interpret it??

chill-filter uses sourmash gather to calculate the results.

See the sourmash gather documentation for more information on the algorithm and the results file!

Can you add a genome to your search database for me?

Please ask in the issue tracker!

You can also deploy a copy of this site locally, with custom databases; see the chill-filter source code README for details.

How do I cite chill-filter?

For now, please cite the sourmash paper in the Journal of Open Source Software:

Irber et al., (2024). sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. Journal of Open Source Software, 9(98), 6830, https://doi.org/10.21105/joss.06830

How do you pay for this?

We're skipping our normal avocado toast brunch order in order to support this site. We hope you appreciate our sacrifice!

What kind of resources are needed to run a chill-filter server?

chill-filter.sourmash.bio is running on a Digital Ocean Basic Droplet, with 4 GB of RAM, 2 CPUs, and 80 GB of SSD space.