From 3f4bfc69e2cada6622fba5065b4c4f8e5a7523dc Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Thu, 7 Nov 2024 11:50:31 +0000 Subject: [PATCH] Clarify threading works at reference genome level Looking at the code in computeCoreIdentity.hpp and splitDatabase.sh it is clear that threading works at the level of reference genomes. This is a very natural implementation, however it was not clear from the README file that there is no benefit with a single reference genome. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5224ab6..6e79303 100644 --- a/README.md +++ b/README.md @@ -104,7 +104,7 @@ Using above commands, we get a plot file fastani.out.visual.pdf displayed below. ### Parallelization -FastANI (v1.1 onwards) supports multi-threading, see the help page on how to configure thread count. To parallelize FastANI beyond single compute node, users also have the choice to simply divide their reference database into multiple chunks, and execute them as parallel processes. We provide a [script](scripts) in the repository to randomly split the database for this purpose. +FastANI (v1.1 onwards) supports multi-threading where multiple reference genomes are provided, see the help page on how to configure thread count. To parallelize FastANI beyond a single compute node, users also have the choice to simply divide their list of reference databases into multiple chunks, and execute them as parallel processes. We provide a [script](scripts) in the repository to randomly split the database for this purpose. ### Troubleshooting