From fd6cac96c3df88f8bda7181d64d9229dde5c1d14 Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Fri, 16 Jul 2021 14:04:02 +0100 Subject: [PATCH] add civet to readme --- resources/publish_readme.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/resources/publish_readme.txt b/resources/publish_readme.txt index 30c2cc7..ec36438 100644 --- a/resources/publish_readme.txt +++ b/resources/publish_readme.txt @@ -29,5 +29,8 @@ - `cog__alignment.fa` : filtered, trimmed alignment with sequences matching those in the corresponding metadata - `cog__metadata.csv` : corresponding metadata for filtered, trimmed alignment with the following columns `"sequence_name", "country","adm1","is_pillar_2","sample_date", "epi_week","lineage","lineages_version"` - +### Civet3 +- `cog_global__private_alignment.fa` : masked, trimmed, filtered alignment of COG and GLOBAL sequences +- `cog_global__private_metadata.csv` : corresponding metadata with the following columns `"sequence_name","gisaid_id","cog_id","source_id","sample_date","epi_week","country","adm1","adm2","suggested_adm2_grouping","outer_postcode","is_surveillance","is_travel_history","travel_history","is_pillar_2","collection_pillar","lineage","lineages_version","scorpio_call"` +- `cog_global__mutations.csv` : metadata file produced by gofasta updown list, providing information about nucleotide mutations and ambiguous regions in aligned sequences