This repository aims to provide consensus sequences, variant calls and depth information for the SRA data associated with BioProjects listed below. The repository checks for new data every 24 hours and updates the consensus sequences, variant calls, depth information, demixed milk samples and associated metadata accordingly. Additionally, the repository updates mapping of consensus genomes to the respective GenBank sequences by sample name every 24 hours.
| BioProject | Description |
|---|---|
| PRJNA1102327 | U.S. H5N1 clade 2.3.4.4b genotype B3.13 immediate releases related to emergence and spread in dairy cattle. |
| PRJNA1122849 | U.S. H5N1 clade 2.3.4.4b immediate releases related to peridomestic animals. |
| PRJNA1134696 | Viral sequencing of US dairy milk. |
| PRJNA1219588 | U.S. H5N1 clade 2.3.4.4b genotype D1.1 immediate releases related to emergence in dairy cattle. |
| PRJNA1207547 | U.S. Influenza A Surveillance in Wildlife. |
| PRJNA980729 | US HPAI Sequencing. |
| Data Type | Description | Location |
|---|---|---|
| Consensus Sequences | Consensus builds from SRA data (min depth: 1, quality: 20, consensus threshold: 50%). | ./fasta/ |
| Variant Calls | Variant calls results from corresponding SRA data. | ./variants/ |
| Depth Information | Depth information for each SRA dataset. | ./depth/ |
| Milk Surveillance | Estimates of lineage abundance from sources like “Bulk milk tanks” using Freyja. | ./demixed/ |
| Genotype Information | Genotyping processed using GenoFLU. | ./metadata/genoflu_results.tsv |
| SRA Metadata | Metadata provided from SRA sources. | ./metadata/SraRunTable_automated.csv |
| Genome to GenBank Mapping | Links consensus genomes to their respective GenBank sequences by sample name. | ./metadata/genbank_mapping.tsv |
For a NextStrain-style formatted version of the genomes and metadata, please see moncla-lab/avian-flu-USDA-cattle/.
The data processing pipeline is available in andersen-lab/flusra.
All data generated from 23rd May 2024 uses the GenBank genome A/cattle/Texas/24-008749-003/2024(H5N1) as a reference. The reference genome can be found in ./reference/. Settings include a minimum depth of 1, minimum quality of 20, and a consensus threshold at 50%.
Note
Prior to 23rd May 2024, consensus genomes for 8 segments were generated using EPI_ISL_19032063 (source: GISAID) as a reference. These were produced with iVar v1.4.2 using the settings (min depth: 1, quality: 20 consensus threshold: 50%).
We invite the scientific community to utilize and scrutinize this data to enhance overall quality. For queries or feedback, please contact us.
Please refer to the NCBI usage policies for more details.
We gratefully acknowledge the authors, originating and submitting laboratory of the sequences from GISAID's EpiFlu™ Database we used as references for our genome assemblies. The list is provided in ./acknowledgements.