Ingest extra sources

README.md

@@ -60,18 +60,25 @@ Note that you may need to remove any existing data in `results/` in order for sn
 
 #### Using locally ingested data (instead of downloading from S3)
 
-Run the pipeline with `--config 'local_ingest=True'` to use the locally available files produced by the ingest pipeline (see `./ingest/README.md` for details on how to run).
-Specifically, the files needed are `ingest/results/metadata.tsv` and `ingest/results/sequences_{SEGMENT}.fasta`.
+Run the pipeline with `--config 'local_ingest=fauna'` to use the locally available files produced by the ingest pipeline (see `./ingest/README.md` for details on how to run).
+Specifically, the files needed are `ingest/results/fauna/metadata.tsv` and `ingest/results/fauna/sequences_{SEGMENT}.fasta`.
+Replace "fauna" with "genome" (or any other namespace which ingest can produce) as needed.
 
 
 #### Running full genome builds
 
-Run full genome builds with the following command.
+Run full genome builds using the data on S3 (fauna) with the following command:
 
-``` bash
+```bash
 nextstrain build . --snakefile Snakefile.genome
 ```
 
+To include non-fauna data first run the "Ingest for whole genome builds" (see `ingest/README.md`) then run:
+```bash
+nextstrain build . --snakefile Snakefile.genome --config 'local_ingest=genome'
+```
+
+
 Currently this is only set up for the "h5n1-cattle-outbreak" build, and restricts the build to a set of strains where we think there's no reassortment (`config/include_strains_h5n1-cattle-outbreak.txt`). Output files will be placed in `results/h5n1-cattle-outbreak/genome`. See `Snakefile.genome` for more details.
 
 

config/include_strains_h5n1-cattle-outbreak.txt

@@ -222,6 +222,9 @@ A/raccoon/NewMexico/24009496002/2024
 
 A/Texas/37/2024
 
+# Following strains are sourced from ingest/source-data
+A/environment/USA/CO-UW-9084466/2024
+
 # Dropping these strains from include due to excess private mutations
 # A/dairycattle/NorthCarolina/24010327002/2024
 # A/dairycattle/Texas/24009495007/2024

ingest/README.md

@@ -28,7 +28,7 @@ nextstrain build \
     .
 ```
 
-This command produces one metadata file, `results/metadata.tsv`, and one sequences file per gene segment like `results/sequences_ha.fasta`.
+This command produces one metadata file, `results/fauna/metadata.tsv`, and one sequences file per gene segment like `results/fauna/sequences_ha.fasta`.
 Each file represents all available subtypes.
 
 Add the `upload_all` target to the command above to run the complete ingest pipeline _and_ upload results to AWS S3.
@@ -56,6 +56,21 @@ nextstrain build . merge_andersen_segment_metadata
 
 The results will be available in `results/andersen-lab/`.
 
+
+### Ingest for whole genome builds
+
+> This section is in flux
+
+To produce ingest files specifically tailored for the whole genome H5N1 cattle outbreak whole genome build, which combines fauna data
+with extra data in `source-data` run the following (you may need rethink credentials as above):
+
+```sh
+nextstrain build . all_genome
+```
+
+The results will be available in `results/genome/`.
+
+
 ## Configuration
 
 ### Environment Variables

ingest/Snakefile

@@ -6,14 +6,23 @@ wildcard_constraints:
     segment = "|".join(config["segments"])
 
 rule all:
+    # As of 2024-05-16 the default ingest only ingests data from fauna
     input:
-        sequences=expand("results/metadata_{segment}.tsv", segment=config["segments"]),
-        metadata="results/metadata.tsv",
+        sequences=expand("results/fauna/sequences_{segment}.fasta", segment=config["segments"]),
+        metadata="results/fauna/metadata.tsv",
 
 rule upload_all:
+    # As of 2024-05-16 the default upload only uploads data from fauna
     input:
-        sequences=expand("s3/sequences_{segment}.done", segment=config["segments"]),
-        metadata="s3/metadata.done",
+        sequences=expand("s3/fauna/sequences_{segment}.done", segment=config["segments"]),
+        metadata="s3/fauna/metadata.done",
+
+rule all_genome:
+    input:
+        sequences=expand("results/genome/sequences_{segment}.fasta", segment=config["segments"]),
+        metadata="results/genome/metadata.tsv",
 
 include: "rules/upload_from_fauna.smk"
 include: "rules/ingest_andersen_lab.smk"
+include: "rules/ingest_genome_data.smk"
+

ingest/rules/ingest_genome_data.smk

@@ -0,0 +1,31 @@
+
+## This ruleset is in flux and will change often
+## Currently it merges hardcoded (committed) source-data with fauna-derived data
+## No checking is done for duplicate strains
+
+rule merge_genome_metadata:
+    input:
+        fauna = "results/fauna/metadata.tsv"
+    params:
+        source_data = "source-data/metadata.tsv"
+    output:
+        metadata = "results/genome/metadata.tsv"
+    shell:
+        """
+        diff <(head -n 1 {params.source_data}) <(head -n 1 {input.fauna}) &&
+            cp {params.source_data} {output.metadata} && \
+            tail -n +2 {input.fauna} >> {output.metadata}
+        """
+
+rule merge_genome_sequences:
+    input:
+        fauna = "results/fauna/sequences_{segment}.fasta"
+    params:
+        source_data = "source-data/sequences_{segment}.fasta"
+    output:
+        metadata = "results/genome/sequences_{segment}.fasta"
+    shell:
+        """
+        cat {params.source_data} {input.fauna} > {output.metadata}
+        """
+

ingest/rules/upload_from_fauna.smk

@@ -1,8 +1,9 @@
 rule download_segment:
     output:
-        sequences = "data/{segment}.fasta",
+        sequences = "data/fauna/{segment}.fasta",
     params:
         fasta_fields = "strain virus accession collection_date region country division location host domestic_status subtype originating_lab submitting_lab authors PMID gisaid_clade h5_clade",
+        output_dir = "data/fauna",
     benchmark:
         "benchmarks/download_segment_{segment}.txt"
     shell:
@@ -12,16 +13,16 @@ rule download_segment:
             --virus avian_flu \
             --fasta_fields {params.fasta_fields} \
             --select  locus:{wildcards.segment} \
-            --path data \
+            --path {params.output_dir} \
             --fstem {wildcards.segment}
         """
 
 rule parse_segment:
     input:
-        sequences = "data/{segment}.fasta",
+        sequences = "data/fauna/{segment}.fasta",
     output:
-        sequences = "results/sequences_{segment}.fasta",
-        metadata = "results/metadata_{segment}.tsv",
+        sequences = "results/fauna/sequences_{segment}.fasta",
+        metadata = "results/fauna/metadata_{segment}.tsv",
     params:
         fasta_fields =  "strain virus isolate_id date region country division location host domestic_status subtype originating_lab submitting_lab authors PMID gisaid_clade h5_clade",
         prettify_fields = "region country division location host originating_lab submitting_lab authors PMID"
@@ -44,10 +45,10 @@ rule merge_segment_metadata:
     for each segment, but that would be a nice improvement.
     """
     input:
-        segments = expand("results/metadata_{segment}.tsv", segment=config["segments"]),
-        metadata = "results/metadata_ha.tsv",
+        segments = expand("results/fauna/metadata_{segment}.tsv", segment=config["segments"]),
+        metadata = "results/fauna/metadata_ha.tsv",
     output:
-        metadata = "results/metadata.tsv",
+        metadata = "results/fauna/metadata.tsv",
     shell:
         """
         python scripts/add_segment_counts.py \
@@ -58,9 +59,9 @@ rule merge_segment_metadata:
 
 rule upload_sequences:
     input:
-        sequences="results/sequences_{segment}.fasta",
+        sequences="results/fauna/sequences_{segment}.fasta",
     output:
-        flag=touch("s3/sequences_{segment}.done"),
+        flag=touch("s3/fauna/sequences_{segment}.done"),
     params:
         s3_dst=config["s3_dst"],
     shell:
@@ -73,9 +74,9 @@ rule upload_sequences:
 
 rule upload_metadata:
     input:
-        metadata="results/metadata.tsv",
+        metadata="results/fauna/metadata.tsv",
     output:
-        flag=touch("s3/metadata.done"),
+        flag=touch("s3/fauna/metadata.done"),
     params:
         s3_dst=config["s3_dst"],
     shell:

ingest/scripts/add_segment_counts.py

@@ -63,7 +63,7 @@ def summary(strain_count):
         row[column]=strain_count[row['strain']]
 
     with open(args.output, 'w') as fh:
-        writer = csv.DictWriter(fh, fieldnames=fieldnames, delimiter='\t')
+        writer = csv.DictWriter(fh, fieldnames=fieldnames, delimiter='\t', lineterminator='\n')
         writer.writeheader()
         for row in rows:
             writer.writerow(row)

ingest/source-data/metadata.tsv

@@ -0,0 +1,2 @@
+strain	virus	isolate_id	date	region	country	division	location	host	domestic_status	subtype	originating_lab	submitting_lab	authors	PMID	gisaid_clade	h5_clade	n_segments
+A/environment/USA/CO-UW-9084466/2024	avian_flu	PP796043	2024-04-XX	North America	Usa	Colorado	Colorado	Environment	domestic	h5n1	University of Washington 	University of Washington	Roychoudhury,P., Han,P., Kong,K., Xie,H., Gamboa,L., Rodriguez-Salas,L., Ellis,S.E., Greninger,A., Bedford,T., Starita,L. and Chu,H.	?	2.3.4.4b	?	8

ingest/source-data/sequences_ha.fasta

@@ -0,0 +1,2 @@
+>A/environment/USA/CO-UW-9084466/2024
+GATCAGATTTGCATTGGTTACCATGCAAACAATTCGACAGAGCAAGTTGACACGATAATGGAAAAGAACGTCACTGTTACACATGCCCAAGACATACTGGAAAAAACACACAACGGGAAGCTATGCGACCTAAATGGGGTGAAGCCACTGATTTTAAAGGACTGCAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGCGACGAATTCATCAGAGTGCCGGAATGGTCTTACATAGTGGAGCGGGCTAACCCAGCTAATGACCTCTGTTACCCAGGGAGCCTCAATGACTATGAAGAACTGAAACACATGTTGAGCAGAATAAATCATTTTGAGAAGATTCAGATCATTCCCAAGAGTTCCTGGCCAAATCATGAAACATCACTAGGGGTGAGCGCAGCTTGTCCATACCAGGGAGCACCCTCCTTTTTCAGAAATGTGGTGTGGCTTATCAAAAAGAACGATGCATACCCAACAATAAAGATAAGCTACAATAATACTAATCGGGAAGATCTCTTGATACTGTGGGGGATTCATCATTCCAACAATGCAGAAGAGCAGACAAATCTCTACAAAAACCCAATCACCTACATTTCAGTTGGAACATCAACTTTAAACCAGAGGKTGGCACCAAAAATAGCTACTAGATCCCAAGTAAACGGGCAACGTGGAAGAATGGACTTCTTCTGGACAATCTTAAAACCAGATGATGCAATCCATTTCGAGAGTAACGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTTAAGAAAGGGGACTCGACAATTATGAAAAGTGGAGTGGAATATGGCCATTGCAACACCAAATGTCAAACCCCAGTAGGTGCGATAAATTCTAGTATGCCATTTCACAACATACATCCTCTCACCATTGGGGAATGCCCCAAATACGTGAAATCAAACAAGTTGGTCCTTGCGACTGGGCTCAGAAATAGTCCTCTAAGAGAAAAGAGAAGAAAAAGAGGTCTGTTTGGGGCGATAGCAGGGTTTATAGAGGGAGGATGGCAGGGAATGGTTGATGGTTGGTATGGGTACCATCATAGCAATGAGCAGGGGAGTGGGTACGCTGCGGACAAAGAATCCACCCAAAAGGCAATAGATGGAGTTACCAATAAGGTCAACTCAATCATTGACAAAATGAACACTCAATTTGAGGCAGTTGGAAGGGAGTTTAATAACTTAGAAAGGAGGATAGAGAATTTGAACAAGAAAATGGAAGACGGATTCCTAGATGTCTGGACATATAATGCTGAACTTCTAGTTCTCATGGAAAACGAGAGGACTCTAGATTTCCATGATTCAAATGTCAAGAACCTTTACGACAAAGTCAGATTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGCTGTTTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTGAGAAATGGGACGTATGACTACCCTCAGTATTCAGAAGAAGCAAGATTAAAAAGAGAAGAAATAAGCGGAGTGAAATTAGAATCAGTAGGAACTTACCAGATACTGTCAATTTATTCAACAGCGGCAAGTTCCCTAGCACTGGCAATCATGATGGCTGGTCTATCTTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGAATTTGCATTTAGATTTATGAGCTCAGATTGTAGTTAAAAACACC

ingest/source-data/sequences_mp.fasta

@@ -0,0 +1,2 @@
+>A/environment/USA/CO-UW-9084466/2024
+GATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCGTCCCGTCGGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTTTGCAGGGAAGAACACCGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAGTGCCCTAAGTGGAACTGGAGACCCAAACAACATGGACAGAGCAGTCAAGTTGTACAGGAAACTGAAGAGAGAGATAACATTCCATGGGGCTAAAGAAGTTGCACTCAGTTACTCAACCGGTGCACTTGCCAGTTGTATGGGTCTCATATACAACAGGATGGGGACGGTGACCGCAGAAGTGGCATTGGGCCTAGTGTGTGCCACCTGTGAACAGATTGCTGATTCACAGCATCGGTCTCACAGACAGATAGCTACCACCACCAACCCACTGATCAGACATGAAAACAGAATGGTTTTGGCCAGTACTACAGCTAAGGCTATGGAGCAGATGGCTGGATCGAGTGAGCAAGCAGTGGAAGCCATGGAGGTTGCTAGTCAGGCTAGGCAGATGGTGCAGGCGATGAGGACCATTGGAACTCATCCTAGCTCCAGTACCGGTCTGAGAGATGATCTCCTTGAAAATTTGCAGGCCTACCAAAAACGGATGGGAGTGCAACTGCAGCGATTCAAGTGATCCTCTCGTTATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGCCTTTTCTTCAAATGCGTTTATCGTCGCCTTAAATACGGTTTGAAAGGAGGGCCTTCTACGGAAGGAGTACCTGAGTCCATGAGGGAAGAGTACCGGCAGGAACAGCAGAGTGCTGTGGATGTTGACAATGGTCATTTTGTCAACATAGAGCTGGAGTAGAAACAAGGTAGTTTTTTACT

ingest/source-data/sequences_na.fasta

@@ -0,0 +1,2 @@
+>A/environment/USA/CO-UW-9084466/2024
+GTATGGTAATTGGGATAGTCAGCTTGATGCTGCAAATTGGGAACATAATCTCAATATGGGTTAGCCATTCAATCCAAACAGGGAATCAATACCAGCCTGAACCATGCAATCAAAGCATCATTACCTATGAGAACAACACCTGGGTAAATCAGACGTATATCAACATCAGCAGTACCAATTTTCTTGCTGAGCAGGCTGTTACTTCGGTAACATTAGCGGGCAATTCATCTCTTTGCCCTATTAGTGGGTGGGCAATATACAGTAAGGACAACGGTATAAGAATTGGGTCTAAGGGGGATGTGTTTGTTATAAGAGAACCATTCATCTCATGCTCCCACTTGGAATGCAGAACCTTTTTCCTGACCCAGGGAGCTCTGCTGAATGACAAACATTCTAATGGGACAGTTAAGGATAGAAGCCCTTATAGAACTTTGATGAGTTGTCCCGTGGGTGAGGCTCCTTCCCCGTACAATTCAAGATTTGAGTCTGTTGCTTGGTCGGCAAGTGCTTGTCATGATGGCATCAGTTGGTTGACAATCGGTATTTCTGGTCCAGACAATGGAGCTGTGGCTGTATTGAAGTACAATGGCATAATAACGGATACTATCAAGAGTTGGAGAAACAACATTTTGAGAACTCAAGAATCTGAATGTGCTTGCGTAAATGGCTCCTGCTTCACCGTAATGACTGATGGACCAAGCAATGGGCAGGCCTCATATAAAATCTTCAAGATAGAGAAAGGGAAAGTTGTCAAATCAGTTGAAATGAATGCCCCTAATTACCACTACGAGGAATGCTCCTGTTATCCTGATGCGGGTGATATTATGTGTGTGTGCAGGGACAATTGGCATGGCTCGAACCGGCCGTGGGTATCTTTTAATCAAAATCTGGAGTATCAAATAGGATATATATGCAGTGGGATTTTCGGGGACAATCCCCGCCCCAATGATGGAACAGGCAGTTGCAGTCCAATGCCCTCTAATGGGGCATATGGGGTAAAAGGGTTTTCATTTAAGTACGGTAATGGGGTTTGGATCGGAAGAACAAAAAGCACTAGTTCCAGAAGCGGCTTTGAGATGATTTGGGATCCGAATGGGTGGACTGAGACGGACAGTAGTTTCTCAGTGAAGCAAGACATTGTAGAAATAACTGACTGGTCAGGATATAGTGGGAGTTTTGTCCAGCATCCAGAACTGACAGGATTAGATTGCATGAGGCCTTGTTTCTGGGTTGAGCTAATTAGAGGGAGGCCCAAAGAGAATACAATTTGGACTAGCGGGAGCAGCATATCCTTTTGTGGTGTAAATAGTGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCACCATTGACAAGTAG

ingest/source-data/sequences_np.fasta

@@ -0,0 +1,2 @@
+>A/environment/USA/CO-UW-9084466/2024
+CTGAGTGACATCCACATCATGGCGTCTCAAGGCACCAAACGATCCTATGAACAAATGGAAACTGGTGGGGAACGCCAGAATGCCACTGAAATCAGAGCATCTGTTGGAAGAATGGTTGGCGGAATCGGGAGATTCTACATACAGATGTGCACTGAGCTCAAACTCAGTGATCACGAAGGGAGGCTGATCCAAAACAGCATAACCATAGAAAGGATGGTTCTCTCGGCATTTGATGAAAGGAGGAACAAGTATCTGGAGGAACATCCCAGTGCTGGAAAGGATCCCAAGAAGACTGGAGGTCCAATCTACAGGAGGAGAGATGGCAAATGGATGAGAGAGTTGATCCTCTACGACAAAGAAGAGATCAGAAGAATTTGGCGTCAAGCTAATAATGGAGAGGATGCAACTGCTGGTCTCACTCACTTGATGATTTGGCATTCCAATCTGAATGATGCCACATACCAGAGAACAAGGGCACTTGTGCGTACTGGAATGGATCCTAGGATGTGCTCACTGATGCAAGGCTCAACCCTCCCTAGGAGATCCGGGGCTGCTGGAGCGGCAGTGAAAGGAGTTGGAACAATGGTGATGGAATTGATTCGAATGATCAAACGAGGAATCAATGATCGGAATTTCTGGAGAGGTGAAAACGGACGGAGAACCAGGATTGCCTACGAGAGAATGTGCAACATCCTCAAGGGAAAGTTCCAAACAGCAGCACAACGAGCAATGATGGACCAAGTGAGGGAAAGCCGGAATCCTGGGAATGCTGAAATTGAAGATCTCATCTTTCTCGCACGATCTGCTCTCATCCTGAGGGGATCAGTGGCTCATAAGTCCTGTCTGCCTGCTTGCGTGTATGGACTTGCTGTAGCCAGTGGATATGACTTTGAAAGAGAGGGATACTCTCTAGTCGGAATTGATCCTTTCCGTCTGCTCCAGAACAGTCAAGTTTTCAGTCTCATCAGACCGAATGAAAATCCAGCTCACAAAAGTCAGCTGGTATGGATGGCATGCCACTCTGCAGCATTTGAGGATCTGAGAGTGTCAAGCTTCATCAGAGGAACAAGAGTAGTCCCAAGAGGACAACTGTCCACCAGAGGAGTTCAGATTGCTTCAAATGAAAACATGGAGACAATGGATTCCAGTACTCTTGAACTGAGGAGCAGATACTGGGCTATAAGAACAAGAAGTGGAGGAAACACCAACCAACAGAGAGCATCTGCAGGACAAATCAGCGTACAGCCCACATTCTCTGTGCAGAGAAACCTCCCATTCGAGAGAGCAACCATCATGGCAGCATTTACGGGAAACACTGAAGGCAGAACTTCAGACATGAGAACTGAGATCATAAGGATGATGGAAAATGCCAGACCTGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAACAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAATTAAAGAAAAATAC

ingest/source-data/sequences_ns.fasta

@@ -0,0 +1,2 @@
+>A/environment/USA/CO-UW-9084466/2024
+GGATTCCAACACTGTGTTAAGCTTTCAGGTAGACTGCTTTCTTTGGCATGTCCGCAAACGATTTGCAGACCAAGAACTGGGTGATGCCCCATTCCTTGACCGGCTCCGCCGAGACCAGAAGTCTCTAAGAGGAAGAGGCAGCACTCTTGGTCTGGACATCGAGACGGCCACTCGTGCTGGGAAGCAGATAGTGGAGAGGATTCTGGAGGAAGAATCCGACGAGGCACTCAAAATGACTATTGCCTCTGTGCCTGCTCCACGCTACCTAACTGACATGACTCTTGAAGAGATGTCAAGAGACTGGTTCATGCTCATGCCCAAGCAAAAAGTGGCAGGCTCCCTCAGTATCAGAATGGACCAGGCGATTATGGATAAGAACATCATACTGAAGGCAAACTTCAGTGTGATCTTCAATCGGCTGGAGACACTAATACTACTCAGAGCTTTCACTGAAGAGGGAGCAATTGTCGGCGAAATTTCACCATTGCCTTCTCTTCCAGGACATACTGATGAGGATGTCAAAAATGCAATTGGGGTCCTCATCGGAGGACTTGAATGGAATGATAACACAGTTCGAGTCTCTGAAACTTTACAGAGATTCGCTTGGAGAAGCAGTAATGAGGATGGGAGACCTCCACTCCCTCCAAAGCAGAAACGGAAAATGGAGAGGACAATTGAGTCAGAAGTTTGAAGAAATAAGGTGGCTGATTGAAGAAGTGCGACACAGACTAAAGATCACAGAAAATAGTTTTGAACAAATAACATTTATGCAAGCCTTACAACTACTGCTTGAAGTGGAGCAAGAGNNNNNNNNNNNNTCGTTTCAGCTTTTTTATYATTAAATAA

ingest/source-data/sequences_pa.fasta

@@ -0,0 +1,2 @@
+>A/environment/USA/CO-UW-9084466/2024
+ATTCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATTGTCGAGCTTGCGGAAAAAGCAATGAAAGAATATGGGGAAGATCCGAAAATCGAGACAAACAAATTTGCCGCAATATGCACACACTTAGAAGTCTGTTTCATGTATTCGGATTTCCATTTTATTGACGAACGAGGCGAATCAATGATTGTAGAATCTGGCGATCCAAATGCATTATTGAAACACCGATTTGAGATAATCGAAGGGAGAGACCGAGCAATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGGGGTCGAAAAGCCCAAATTCCTCCCTGATTTGTATGACTACAGAGAGAACAGATTCATTGAAATTGGAGTAACGCGAAGGGAAGTTCACATATACTATTTGGAAAAAGCCAACAAGATAAAATCAGAGAAAACACATATTCACATATTCTCATTCACTGGAGAGGAAATGGCCACCAAGGCGGACTACACCCTTGATGAAGAGAGCAGAGCAAGAATAAAAACCAGACTGTTCACTATAAGACAAGAAATGGCCAGTAGAGGTCTATGGGATTCCTTTCGTCAATCCGAGAGAGGCGAAGAGACAATTGAAGAAAGATTTGAAATCACAGGAACCATGCGCAGGCTTGCCGACCAAAGTATTCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAGGTGAACGCCAGAATTGAGCCATTTCTGAAGACAACACCACGCCCTCTCAGATTACCTGATGGGCCTCCCTGTCCTCAGCGGTCGAAGTTCTTGCTGATGGATGCCCTTAAGTTGAGCATCGAAGACCCTAGTCATGAGGGGGAGGGCATACCGCTGTATGATGCAATCAAATGCATGAAGACATTTTTTGGCTGGAAAGAGCCCAACATCGTAAAGCCGCATGAGAAAGGCATAAACCCTAATTACCTCCTGGCTTGGAAGCAGGTGCTGGCAGAACTTCAAGACATTGAAAATGAGGAGAAAATTCCAAAAACAAAGAACATGAAGAAAACAAGCCAATTGAAGTGGGCACTTGGTGAGAACATGGCTCCAGAAAAAGTGGACTTTGAGGACTGCAAAGATGTTAGCGATCTAAGACAGTACGACAGTGACGAACCAGAGTCTAGATCACTAGCAAGCTGGATTCAGAGTGAATTCAACAAGGCATGCGAACTGACAGATTCGAGTTGGATTGAACTTGATGAGATAGGGGAAGACGTTGCTCCAATCGAACACATTGCGAGTGTGAGGAGGAACTATTTCACAGCGGAGGTATCCCATTGCAGGGCCACTGAATACATAATGAAGGGAGTATACATAAACACAGCCCTATTGAATGCATCCTGTGCAGCCATGGATGACTTCCAATTGATTCCAATGATAAGTAAGTGCAGAACTAAAGAAGGAAGACGGAGGACAAATCTGTATGGATTCATTATAAAAGGAAGATCCCATTTGAGGAATGACACCGATGTGGTAAACTTTGTGAGCATGGAATTCTCTCTAACTGACCCGAGGCTAGAGCCACACAAATGGGAAAARTACTGTGTTCTTGAAATAGGAGACATGCTATTGAGGACTGCGATAGGTCAAGTGTCGAGGCCCATGTTCCTRTATGTGAGAACCAATGGAACYTCCAARATCAARATGAAATGGGGCATGGARATGAGGCGMTGCCTTCTTCAGTCCCTTCAACAAATTGAGAGCATGATTGAGGCCGAATCTTCTGTCAAAGAGAAGGACATGTCCAAGGAATTCTTTGAAAACAAATCAGAAACATGGCCAATTGGAGAATCACCCAAAGGGGTGGAGGAAGGCTCTATTGGGAAAGTATGCAGAACATTGCTAGCAAAGTCTGTGTTCAACAGCCTATATGCATCTCCTCAACTCGAGGGGTTTTCAGCTGAATCAAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGAACCTGGAACCTTCGATCTTGGGGGGCTATATGAAGCAATTGAGGAGTGCCTGATTAACGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTGAAATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAACAAGGTACTTTTTTGGAC

ingest/source-data/sequences_pb1.fasta

@@ -0,0 +1,2 @@
+>A/environment/USA/CO-UW-9084466/2024
+GAATGGATGTCAATCCGACCTTACTCTTCTTGAAAGTTCCAGCGCAAAATGCCATAAGCACCACATTCCCGTATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGATATACCATGGACACAGTTAACAGAACACATCAATATTCAGAAAAAGGGAAATGGACAACAAACTCAGAAACCGGGGCACCTCAACTCAATCCAATTGATGGACCATTGCCTGATGACAATGAGCCAAGTGGATATGCACAAACGGACTGCGTCCTTGAAGCAATGGCTTTCCTTGAAGAATCCCATCCAGGAATCTTTGAAAACTCGTGTCTTGAAACGATGGAAGTTGTTCAACAAACAAGAGTGGACAAGTTGACCCAAGGCCGTCAGACTTATGATTGGACATTAAACAGAAATCAGCCGGCTGCAACTGCATTAGCTAATACTATAGAGGTCTTCAGATCGAACGGTCTTACAGCTAATGAATCAGGAAGGCTAATAGATTTCCTCAAGGATGTGGTGGAATCAATGGATAAAGAGGAAATAGAAATAACAACGCATTTCCAAAGGAAAAGAAGAGTGAGAGACAACATGACCAAGAAAATGGTCACACAACGGACGATAGGAAAGAAGAAACAAAGGTTAAACAAAAGGAGCTATCTGATAAGAGCATTGACACTGAACACAATGACAAAAGACGCCGAAAGAGGCAAATTAAAGAGAAGGGCAATTGCAACACCCGGAATGCAAATCAGAGGGTTTGTGTACTTTGTTGAAACATTAGCAAGGAGCATTTGTGAGAAACTTGAACAATCTGGACTCCCAGTTGGAGGCAATGAAAAGAAGGCCAAACTAGCAAATGTTGTGAGAAAGATGATGACTAATTCGCAAGACACAGAGCTCTCTTTCACAATCACGGGAGACAACACTAAATGGAATGAGAACCAGAATCCTAGGATGTTTCTGGCAATGATAACATAYATWACAAGGAACCAACCTGAATGGTTCAGGAATGTATTGAGCATTGCACCTATAATGTTCTCAAACAAAATGGCAAGACTAGGGAAAGGATACATGTTCGAAAGTAAGAGCATGAAGCTTCGAACACAAATACCGGCAGAAATGCTAGCGAGCATTGATCTGAAATACTTCAATGAGTCAACAAGGAAGAAAATAGAGAAGATAAGACCTCTTCTAATAGATGGTACGGCCTCATTAAGCCCTGGAATGATGATGGGCATGTTCAACATGCTGAGTACAGTTCTGGGAGTTTCGATTCTAAATCTAGGGCAAAAGAAGTACACCAAAACAACATACTGGTGGGATGGACTACAATCTTCTGATGACTTTGCTCTCATCGTGAATGCTCCAAATCATGAGGGAATACAAGCAGGAGTAGACAGATTCTATAGAACCTGCAAGCTGGTAGGAATCAATATGAGCAAAAAGAAGTCATACATAAACAGGACAGGAACATTTGAATTCACAAGTTTTTTCTATCGCTATGGATTTGTAGCCAATTTCAGCATGGAGTTGCCCAGCTTTGGAGTTTCTGGGATCAATGAATCTGCAGACATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATCAACAATGATCTTGGACCAGCAACAGCCCAAATGGCTCTACAGCTATTCATCAAGGATTACAGATACACATATCGATGTCACAGAGGAGACACACAAATTCAAACAAGGAGGTCATTCGAGCTGAAAAAGTTATGGGAACAAACCCGCTCAAAACCAGGACTGCTGGTCTCAGATGGAGGGCCAAATCTATACAATATCCGAAATCTCCACATTCCGGAAGTCTGCTTAAAATGGGAGCTAATGGACGAAGACTATCAGGGAAGGCTTTGTAATCCCCTGAATCCGTTTGTAAGCCACAAAGAAATAGAGTCTGTGAACAATGCTGTGGTGATGCCAGCTCATGGCCCAGCTAAGAGTATGGAATATGATGCTGTTGCCACCACTCACTCCTGGATCCCTAAGAGGAACCGCTCTATTCTTAATACAAGCCAAAGGGGAATCCTTGAAGACGAACAGATGTATCAAAAGTGCTGCAATCTATTTGAAAAATTCTTCCCTAGCAGTTCATACAGGAGGCCGGTTGGAATTTCCAGCATGGTGGAGGCCATGGTTTCTAGGGCCCGAATTGATGCACGAATTGACTTCGAATCTGGACGGATTAAGAAGGAGGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAGAAATAGTGAATTTAGCTTGTCCTTCATGAAAAAATG