From 925b3e429d458df40cf75728b126ff1cd335f23a Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 28 Nov 2023 14:21:33 -0700 Subject: [PATCH 1/2] add FAQ to sidebar --- doc/sidebar.md | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/sidebar.md b/doc/sidebar.md index faa990a2f6..8fefe519a6 100644 --- a/doc/sidebar.md +++ b/doc/sidebar.md @@ -38,6 +38,7 @@ X and Linux. They require about 5 GB of disk space and 5 GB of RAM. * [Publications about sourmash](publications.md) * [A guide to the internal design and structure of sourmash](sourmash-internals.md) * [Funding acknowledgements](funding.md) +* [Frequently asked questions](faq.md) ## Developing and extending sourmash From 4cb056fd971bed4215365701d726e049f84ecdeb Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 28 Nov 2023 14:21:52 -0700 Subject: [PATCH 2/2] add memory usage vs ksize to FAQ --- doc/faq.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/doc/faq.md b/doc/faq.md index 88af9dc82c..522df3b64f 100644 --- a/doc/faq.md +++ b/doc/faq.md @@ -245,3 +245,14 @@ read mapping between the metagenome and the relevant reference genome or, if you are interested in retrieving accessory elements, you can try out [spacegraphcats](https://spacegraphcats.github.io/spacegraphcats/02-spacegraphcats-use-cases/). + +## How does memory usage for sourmash change with k-mer size? + +sourmash hashes k-mers into 64-bit numbers, so the size of what is +stored is independent of the k-mer size. The only impact of k-mer size +on sourmash behavior is then more on the biology side - how many +matches do you gain (or lose) with that k-mer size? And do you have a +lot of new k-mers that pop up with a longer k-mer size (e.g. because +of included variation)? These questions must be answered by experimentation +and may be data-set specific. +