adding in a key to translate strain name into bioproject accession

blab · Aug 14, 2021 · 3a27ea8 · 3a27ea8
1 parent 3309d15
commit 3a27ea8
Show file tree

Hide file tree

Showing 2 changed files with 169 additions and 4 deletions.
diff --git a/data/README.md b/data/README.md
@@ -1,6 +1,4 @@
 ## Consensus genomes 
-We are releasing draft genome sequences of mumps virus that were sequenced from PCR-positive diagnostic specimens collected by the Washington State Department of Health. We intend to use these sequence data to conduct an investigation into mumps virus transmission in Washington state, outbreak seeding and spread, and epidemiological drivers of transmission. We are releasing these genomes in the hope that they are useful for those individuals involved in the public health response to mumps and to other groups working to understand mumps virus transmission and evolution.
+These consensus genomes represent those generated from a mumps outbreak in Washington in 2016, in addition to a sampling of mumps genomes collected from all over the US from 2006 to present. These genomes were used in a [paper describing the mumps outbreak](https://elifesciences.org/articles/66448#content), and have also been deposited in public databases for others to use. Consensus genomes are freely available in Genbank under accession numbers [MT859507-MT859672](ncbi.nlm.nih.gov/nuccore/?term=MT859507%3AMT859672%5Baccn%5D), and raw fastq files with all human reads removed are available on the Short Read Archive under BioProject [PRJNA641715](https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA641715). A key that links the strain names as shown in this repository to the bioproject accessions is available [here](). 
 
-This work represents a pre-publication sharing of pathogen genomic data of public health significance. We believe that open sharing of sequence data and early analyses is necessary to inform public health response in a timely fashion. We encourage other investigators to use these data in their own analyses to better contextualize their work. All we ask is that you let us know if you plan to use these data in a publication. Please email us with any questions or comments at trevor@bedford.io.  
-
-We have renamed strains a few times during the process of this project. All sequences currently here contain the strain names that will be uploaded to Genbank and the SRA, as well as used on nextstrain.org/mumps. However, if you accessed and used these genomes previously, we have included a name key to convert between these new strain names and the ones listed previously. 
+During the process of doing this project, we renamed strains a few times. All sequences currently here contain the strain names as used and displayed on nextstrain.org/mumps and as deposited in Genbank. However, if you accessed and used these genomes previously, we have included a [name key](https://github.com/blab/mumps-seq/blob/master/data/consensus-genomes/strain-names-key-2020-06-15.fasta) to convert between these new strain names and the ones listed previously.