From 2be75918a9de403eee6eb5f2c381d8170624b0ff Mon Sep 17 00:00:00 2001 From: Albert Tian Chen Date: Tue, 7 Sep 2021 09:14:59 -0400 Subject: [PATCH] Update README.md Update docs to reflect change from bowtie2 to minimap2 --- README.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/README.md b/README.md index 58749504b..af8bdab59 100644 --- a/README.md +++ b/README.md @@ -213,9 +213,7 @@ cd workflow_main snakemake --configfile ../config/config_genbank.yaml ``` -This pipeline will align sequences to the reference sequence with `bowtie2`, extract SNVs on both the NT and AA level, and combine all metadata and SNV information into one file: `data_package.json.gz`. - -**NOTE**: `bowtie2`, the sequence aligner we use, usually uses anywhere from 8 – 10 GB of RAM per CPU during the alignment step. If the pipeline includes the alignment step, then only use as many cores as you have RAM / 10. i.e., if your machine has 128 GB RAM, then you can run at most 128 / 10 ~= 12 cores. +This pipeline will align sequences to the reference sequence with `minimap2`, extract SNVs on both the NT and AA level, and combine all metadata and SNV information into one file: `data_package.json.gz`. To pass this data onto the front-end application, host the `data_package.json.gz` file on an accessible endpoint, then specify that endpoint in the `data_package_url` field in the `config/config_[workflow]` file that you are using.