From 338719f6ca2934ace124e7f71c0092172415b6c0 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Mon, 16 Oct 2023 11:29:27 -0700 Subject: [PATCH] doc: ncbi datasets --- ingest/README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ingest/README.md b/ingest/README.md index ec571d0d..a94ff53b 100644 --- a/ingest/README.md +++ b/ingest/README.md @@ -2,6 +2,10 @@ This is the ingest pipeline for mpox virus sequences. +## Software requirements + +Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools. + ## Usage > NOTE: All command examples assume you are within the `ingest` directory. @@ -83,8 +87,7 @@ These are optional environment variables used in our automated pipeline for prov ### GenBank data -GenBank sequences and metadata are fetched via NCBI Virus. -The exact URL used to fetch data is constructed by `vendored/ncbi-virus-url`. +GenBank sequences and metadata are fetched via [NCBI datasets](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/). ## `ingest/vendored`