From 5e57bef97922b4178c433566ca01cbb2de554ea8 Mon Sep 17 00:00:00 2001 From: "N. Tessa Pierce-Ward" Date: Wed, 7 Feb 2024 14:30:29 -0800 Subject: [PATCH 1/3] add branchwater reference; make FAQ more visible --- doc/faq.md | 3 +++ doc/index.md | 8 +++++++- doc/sidebar.md | 5 ++++- 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/doc/faq.md b/doc/faq.md index df17c5672..50857a84e 100644 --- a/doc/faq.md +++ b/doc/faq.md @@ -302,3 +302,6 @@ 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. +## Can sourmash run multi-threaded? + +sourmash is currently single-threaded, but the [branchwater plugin for sourmash](https://github.com/sourmash-bio/sourmash_plugin_branchwater) provides faster and lower-memory multithreaded implementations of several important sourmash features - sketching, searching, and gather (metagenome decomposition). It does so by implementing higher-level functions in Rust on top of the core Rust library of sourmash. As a result it provides some of the same functionality as sourmash, but 10-100x faster and in 10x lower memory. Note that this code is functional and tested, but does not have all of the features of sourmash. Code and features will be integrated back into sourmash as they mature. diff --git a/doc/index.md b/doc/index.md index 20e5d4f9f..ab8577b53 100644 --- a/doc/index.md +++ b/doc/index.md @@ -58,6 +58,8 @@ sourmash is inspired by [mash](https://mash.readthedocs.io), and supports most mash analyses. sourmash also implements an expanded set of functionality for metagenome and taxonomic analysis. +While sourmash is currently single-threaded, the [branchwater plugin for sourmash](https://github.com/sourmash-bio/sourmash_plugin_branchwater) provides faster and lower-memory implementations of several important sourmash features - sketching, searching, and gather (metagenome decomposition). It does so by implementing higher-level functions in Rust on top of the core Rust library of sourmash. As a result it provides some of the same functionality as sourmash, but 10-100x faster and in 10x lower memory. Note that this code is functional and tested, but does not have all of the features of sourmash. Code and features will be integrated back into sourmash as they mature. + sourmash development was initiated with a grant from the Moore Foundation under the Data Driven Discovery program, and has been supported by further funding from the NIH and NSF. Please see @@ -94,6 +96,10 @@ X and Linux. They require about 5 GB of disk space and 5 GB of RAM. * [A short guide to using sourmash output with R](other-languages.md). +## Frequently Asked Questions + +* [Frequently asked questions](faq.md) + ### How sourmash works under the hood * [An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.ipynb) @@ -128,6 +134,6 @@ hidden: true sidebar command-line -api-example databases +api-example ``` diff --git a/doc/sidebar.md b/doc/sidebar.md index 5e81538fb..f4e6e8170 100644 --- a/doc/sidebar.md +++ b/doc/sidebar.md @@ -25,6 +25,10 @@ X and Linux. They require about 5 GB of disk space and 5 GB of RAM. * [A short guide to using sourmash output with R](other-languages.md). +## Frequently Asked Questions + +* [Frequently asked questions](faq.md) + ## How sourmash works under the hood * [An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.ipynb) @@ -38,7 +42,6 @@ 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 f90788c645d13a98a2116c4bfff11d9a6b9a6540 Mon Sep 17 00:00:00 2001 From: "N. Tessa Pierce-Ward" Date: Wed, 7 Feb 2024 14:33:20 -0800 Subject: [PATCH 2/3] upd wording --- doc/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/index.md b/doc/index.md index ab8577b53..6b3e0e21f 100644 --- a/doc/index.md +++ b/doc/index.md @@ -58,7 +58,7 @@ sourmash is inspired by [mash](https://mash.readthedocs.io), and supports most mash analyses. sourmash also implements an expanded set of functionality for metagenome and taxonomic analysis. -While sourmash is currently single-threaded, the [branchwater plugin for sourmash](https://github.com/sourmash-bio/sourmash_plugin_branchwater) provides faster and lower-memory implementations of several important sourmash features - sketching, searching, and gather (metagenome decomposition). It does so by implementing higher-level functions in Rust on top of the core Rust library of sourmash. As a result it provides some of the same functionality as sourmash, but 10-100x faster and in 10x lower memory. Note that this code is functional and tested, but does not have all of the features of sourmash. Code and features will be integrated back into sourmash as they mature. +While sourmash is currently single-threaded, the [branchwater plugin for sourmash](https://github.com/sourmash-bio/sourmash_plugin_branchwater) provides faster and lower-memory multithreaded implementations of several important sourmash features - sketching, searching, and gather (metagenome decomposition). It does so by implementing higher-level functions in Rust on top of the core Rust library of sourmash. As a result it provides some of the same functionality as sourmash, but 10-100x faster and in 10x lower memory. Note that this code is functional and tested, but does not have all of the features of sourmash. Code and features will be integrated back into sourmash as they mature. sourmash development was initiated with a grant from the Moore Foundation under the Data Driven Discovery program, and has been From cab6f4cd1a80ef6a971c7eef6983f51e0dd75cdb Mon Sep 17 00:00:00 2001 From: Tessa Pierce Ward Date: Thu, 8 Feb 2024 15:31:18 -0800 Subject: [PATCH 3/3] Update doc/faq.md Co-authored-by: C. Titus Brown --- doc/faq.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/faq.md b/doc/faq.md index 50857a84e..d8d9da062 100644 --- a/doc/faq.md +++ b/doc/faq.md @@ -302,6 +302,6 @@ 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. -## Can sourmash run multi-threaded? +## Can sourmash run with multiple theads? sourmash is currently single-threaded, but the [branchwater plugin for sourmash](https://github.com/sourmash-bio/sourmash_plugin_branchwater) provides faster and lower-memory multithreaded implementations of several important sourmash features - sketching, searching, and gather (metagenome decomposition). It does so by implementing higher-level functions in Rust on top of the core Rust library of sourmash. As a result it provides some of the same functionality as sourmash, but 10-100x faster and in 10x lower memory. Note that this code is functional and tested, but does not have all of the features of sourmash. Code and features will be integrated back into sourmash as they mature.