diff --git a/doc/faq.md b/doc/faq.md index df17c5672..d8d9da062 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 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. diff --git a/doc/index.md b/doc/index.md index 20e5d4f9f..6b3e0e21f 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 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 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