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Ingest from NCBI Virus + NCBI Datasets #40

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merged 36 commits into from
May 30, 2024
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Ingest from NCBI Virus + NCBI Datasets #40

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84e88e6
ingest: Copy pathogen-repo-guide/ingest to build-configs/ncbi/
joverlee521 May 22, 2024
44af3f7
ingest/build-configs/ncbi: remove unused files & boilerplate text
joverlee521 May 22, 2024
4d6a8c8
ingest: Connect NCBI ingest with main workflow
joverlee521 May 22, 2024
e9c019e
ingest/build-configs/ncbi: Add required options for NCBI Datasets
joverlee521 May 22, 2024
3c491c9
ingest/build-configs/ncbi: README cleanup
joverlee521 May 22, 2024
a2b01e7
git subrepo pull (merge) --force ingest/vendored
joverlee521 May 28, 2024
0143767
Copy NCBI Virus scripts from nextstrain/ingest
joverlee521 May 21, 2024
0eae3e6
ingest/bin/ncbi-virus-url: pull additional fields
joverlee521 May 21, 2024
44b7c41
ingest/bin/fetch-from-ncbi-virus: Output as CSV
joverlee521 May 21, 2024
c506aa8
ingest/build-configs/ncbi: Add rules to fetch from NCBI Virus
joverlee521 May 21, 2024
32ab5ab
ingest/build-configs/ncib: Add transform-segment
joverlee521 May 24, 2024
d5db437
ingest/build-configs/ncbi: Split curated data by segment
joverlee521 May 24, 2024
99b2c9b
ingest/build-configs/ncbi: Add step to dedup within segment
joverlee521 May 24, 2024
e785416
ingest/build-configs/ncbi: Match fauna metadata output
joverlee521 May 25, 2024
78f4ee7
ingest/build-configs/ncbi: Add transform-host
joverlee521 May 25, 2024
f2cf349
Snakemake.genome/filter: Add log output for debugging
joverlee521 May 25, 2024
1540385
rules/common.smk: Add `INGEST_SOURCE`
joverlee521 May 28, 2024
1e17ea6
Switch h5n1-cattle-outbreak to NCBI data source
joverlee521 May 29, 2024
1b4430a
h5n1-cattle-outbreak: Add more dropped strains
joverlee521 May 29, 2024
7a08f1e
README: Update instructions for h5n1-cattle-outbreak
joverlee521 May 29, 2024
eb11d2e
ingest/build-configs/ncbi: Include `genbank_accession` in metadata ou…
joverlee521 May 29, 2024
f3e3269
h5n1-cattle-outbreak: Use separate description.md
joverlee521 May 29, 2024
df66146
Trim down H5N1 cattle outbreak description
trvrb May 29, 2024
409f850
Remove unused colorings from cattle outbreak Auspice config
trvrb May 29, 2024
88b1f1d
ingest/build-configs/ncbi: Fix transform-to-match-fauna
joverlee521 May 29, 2024
d06a489
ingest/build-configs/ncbi: Use `strain` for annotations
joverlee521 May 29, 2024
19bc00e
ingest/build-configs/ncbi: Add `parse-metadata-from-strain`
joverlee521 May 29, 2024
64d8d99
ingest/build-configs/ncbi: Add to host-map.tsv
joverlee521 May 29, 2024
b267446
ingest/build-configs/ncbi: Add location for A/environment/USA/CO-UW-9…
joverlee521 May 29, 2024
03f401e
Update README under ingest
trvrb May 29, 2024
5b51817
Include additional annotations
trvrb May 29, 2024
f04d275
ingest/build-configs/ncbi: Fix annotations format
joverlee521 May 30, 2024
67c34f2
ingest: Update geolocation_rules.tsv
joverlee521 May 30, 2024
708c61b
Snakefile.genome/refine: Add comments on root_strain
joverlee521 May 30, 2024
d4b9693
Various nits
joverlee521 May 30, 2024
66e1903
ingest/build-configs/ncbi: Switch unnecessary `>>` to `>`
joverlee521 May 30, 2024
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20 changes: 12 additions & 8 deletions README.md
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Expand Up @@ -16,26 +16,26 @@ nextstrain build --aws-batch --aws-batch-cpus 16 --aws-batch-memory 28800 . --jo

Please see [nextstrain.org/docs](https://nextstrain.org/docs) for details about augur and pathogen builds.

## Creating a custom build
## Creating a custom build
The easiest way to generate your own, custom avian-flu build is to use the quickstart-build as a starting template. Simply clone the quickstart-build, run with the example data, and edit the Snakefile to customize. This build includes example data and a simplified, heavily annotated Snakefile that goes over the structure of Snakefiles and annotates rules and inputs/outputs that can be modified. This build, with it's own readme, is available [here](https://github.com/nextstrain/avian-flu/tree/master/quickstart-build).

### Features unique to avian flu builds

#### cleavage site annotations
Influenza virus HA is translated as a single peptide (HA0) that is cleaved to form the mature, functional form (HA1 and HA2). In all human strains and many avian strains, the cleavage site is composed of a single, basic amino acid residue. However, some avian influenza subtypes, particularly H5s, have acquired additional basic residues immediately preceding the HA cleavage site. In some cases, this results in addition of a furin cleavage motif, allowing HA to be cleaved by furin, which is ubiquitously expressed, and allows for viral replication across a range of tissues. The addition of this "polybasic cleavage site" is one of the prime determinants of avian influenza virulence. In these builds, we have annotated whether strains contain a furin cleavage motif, defined here as the sequence `R-X-K/R-R` immediately preceding the start of HA2, where `X` can be any amino acid. We have also added a color by for the cleavage site sequence, which we define here as the 4 bases preceding HA2.
#### cleavage site annotations
Influenza virus HA is translated as a single peptide (HA0) that is cleaved to form the mature, functional form (HA1 and HA2). In all human strains and many avian strains, the cleavage site is composed of a single, basic amino acid residue. However, some avian influenza subtypes, particularly H5s, have acquired additional basic residues immediately preceding the HA cleavage site. In some cases, this results in addition of a furin cleavage motif, allowing HA to be cleaved by furin, which is ubiquitously expressed, and allows for viral replication across a range of tissues. The addition of this "polybasic cleavage site" is one of the prime determinants of avian influenza virulence. In these builds, we have annotated whether strains contain a furin cleavage motif, defined here as the sequence `R-X-K/R-R` immediately preceding the start of HA2, where `X` can be any amino acid. We have also added a color by for the cleavage site sequence, which we define here as the 4 bases preceding HA2.

#### clade labeling
H5 viruses are classified into clades, which are currently viewable as a color by on [nextstrain.org](https://nextstrain.org/avian-flu/h5n1/ha?c=h5_label_clade). Because clade annotations are not available in all public databases, we annotate sequences with their most likely clade using a tool developed by Samuel S. Shepard at CDC called [LABEL](https://wonder.cdc.gov/amd/flu/label/). The assigned clade for each H5N1 or H5Nx sequence are available as public tsvs [here](https://github.com/nextstrain/avian-flu/tree/master/clade-labeling).

To update the `clades.tsv` file with clade annotations for new sequences, run:
To update the `clades.tsv` file with clade annotations for new sequences, run:

`snakemake -s Snakefile.clades -p --cores 1`

To run the builds on without updating the clades file, run:
To run the builds on without updating the clades file, run:

`snakemake -p --cores 1`

To string these together and update the `clades.tsv` file for new sequences and then run the builds:
To string these together and update the `clades.tsv` file for new sequences and then run the builds:

`snakemake -s Snakefile.clades -p --cores 1 && snakemake -p --cores 1`

Expand Down Expand Up @@ -69,10 +69,14 @@ Specifically, the files needed are `ingest/results/metadata.tsv` and `ingest/res
Run full genome builds with the following command.

``` bash
nextstrain build . --snakefile Snakefile.genome
nextstrain build . --snakefile Snakefile.genome --config local_ingest=True ingest_source=ncbi
```

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.
Currently this is only set up for the "h5n1-cattle-outbreak" build using locally ingested NCBI data,
and the build is restricted to a set of strains where we think there's no reassortment, with outgroups
excluded in (`config/dropped_strains_h5n1-cattle-outbreak.txt`).
Output files will be placed in `results/h5n1-cattle-outbreak/genome`.
See `Snakefile.genome` for more details.


### To modify this build to work with your own data
Expand Down
12 changes: 10 additions & 2 deletions Snakefile.genome
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@@ -1,5 +1,8 @@
include: "rules/common.smk"

assert LOCAL_INGEST == True and INGEST_SOURCE == "ncbi", \
"Full genome build is only set up for local ingest from 'ncbi'."

import json

# -------------------- notes --------------------
Expand Down Expand Up @@ -32,7 +35,7 @@ rule files:
colors = lambda w: f"config/colors_{subtype(w.build_name)}.tsv",
lat_longs = lambda w: f"config/lat_longs_{subtype(w.build_name)}.tsv",
auspice_config = "config/auspice_config_{build_name}.json",
description = "config/description.md"
description = "config/description_{build_name}.md"

files = rules.files.params

Expand All @@ -47,6 +50,7 @@ rule filter:
query = 'region == "North America"'
output:
sequences = "results/{build_name}/genome/sequences_{segment}.fasta"
log: "logs/{build_name}/genome/sequences_{segment}.txt"
shell:
"""
augur filter \
Expand All @@ -56,6 +60,7 @@ rule filter:
--exclude {input.exclude} \
--min-date {params.min_date} \
--query {params.query:q} \
--output-log {log} \
--output-sequences {output.sequences}
"""

Expand Down Expand Up @@ -148,6 +153,7 @@ def clock_rate(w):
stdev = mean/2
return f"--clock-rate {mean} --clock-std-dev {stdev}"


rule refine:
message:
"""
Expand All @@ -167,7 +173,9 @@ rule refine:
coalescent = "const",
date_inference = "marginal",
clock_rate = clock_rate,
root_strain = "A/skunk/NewMexico/24006483001/2024"
# Using the closest outgroup as the root
# Make sure this strain is force included via augur filter --include
root_strain = "A/skunk/NewMexico/24-006483-001/2024"
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is it worth a comment here about why this strain for the root? feels kinda magic-number-y

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It's the closest outgroup.

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Added comment in b477716

shell:
"""
augur refine \
Expand Down
26 changes: 6 additions & 20 deletions config/auspice_config_h5n1-cattle-outbreak.json
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Expand Up @@ -11,7 +11,8 @@
"url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1102327"
},
{
"name": "GISAID"
"name": "GenBank",
"url": "https://www.ncbi.nlm.nih.gov/genbank/"
}
],
"colorings": [
Expand Down Expand Up @@ -45,26 +46,11 @@
"title": "Host",
"type": "categorical"
},
{
"key": "domestic_status",
"title": "Domestic or Wild",
"type": "categorical"
},
{
"key": "subtype",
"title": "Subtype",
"type": "categorical"
},
{
"key": "h5_label_clade",
"title": "Provisional LABEL Clade",
"type": "categorical"
},
{
"key": "gisaid_clade",
"title": "GISAID Clade",
"type": "categorical"
},
{
"key": "furin_cleavage_motif",
"title": "Furin Cleavage Motif",
Expand Down Expand Up @@ -103,15 +89,15 @@
},
"filters": [
"host",
"domestic_status",
"region",
"country",
"division",
"subtype",
"h5_label_clade",
"gisaid_clade",
"authors",
"author",
"originating_lab",
"submitting_lab"
],
"metadata_columns": [
"genbank_accession"
]
}
3 changes: 3 additions & 0 deletions config/description_h5n1-cattle-outbreak.md
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@@ -0,0 +1,3 @@
We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.

Genomic data from the ongoing outbreak of H5N1 in cattle in the US was shared by the [National Veterinary Services Laboratories (NVSL)](https://www.aphis.usda.gov/labs/about-nvsl) of the [Animal and Plant Health Inspection Service (APHIS)](https://www.aphis.usda.gov/) of the U.S. Department of Agriculture (USDA) in an open fashion to NCBI GenBank.
227 changes: 97 additions & 130 deletions config/dropped_strains_h5n1-cattle-outbreak.txt
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@@ -1,135 +1,102 @@
A/chicken/Scotland/1959
A/mallard/Poland/141/2015 # overly divergent
A/Chicken/Egypt/AR528/2017
A/mink/EasternChina/0712/2018 # divergent
A/chicken/Dakahlia/110/2007 # divergent
A/chicken/Pessel/BPPVRII/2007 # divergent
A/duck/China/E26/2012 # divergent
A/Fox/Bayern/WS113/2022
A/mallard/Denmark/091795/2022
A/Mallard/Netherlands/8/2023
A/kelpgull/Chile/C35523/2017
A/egret/Korea/22WC603/2023
A/chicken/Poland/003/2020
A/chicken/Scotland/128320/2023

# Duplicated entries in GISAID
A/blackbird/Texas/24008354001original/2024
A/blackbird/Texas/24008357001original/2024
A/commongrackle/Texas/24008356001original/2024
A/commongrackle/Texas/24008356003original/2024
A/feline/Montana/24009038001/2024
A/feline/Texas/2402932901/2024
A/feline/Texas/2402932902/2024
A/feline/USA/24008764001original/2024
A/feline/USA/24008764002original/2024
A/feline/USA/24008850001original/2024
A/feline/USA/24008850002original/2024
A/feline/USA/24009116002original/2024
A/feline/USA/24009116004original/2024
A/feline/USA/24009116005original/2024
A/feline/USA/24009311004original/2024
A/feline/USA/24009311006original/2024
A/goat/Minnesota/24007234009original/2024
A/peregrinefalcon/California/24005915001original/2024
A/skunk/NewMexico/24006483001original/2024

# Dropping these strains from include due to excess private mutations
A/dairycattle/NorthCarolina/24010327002/2024
A/dairycattle/Texas/24009495007/2024
A/domesticcat/NewMexico/24009116001/2024
A/cattle/NorthCarolina/24-010327-002/2024
A/cattle/Texas/24-009495-007/2024
A/domesticcat/NewMexico/24-009116-001/2024

# These strains are basal to the outbreak and we exclude them to avoid low-confidence DTA reconstruction.
A/Canadagoose/Wyoming/24003692001original/2024
A/Peregrinefalcon/California/24005915001/2024
A/Canadagoose/Wyoming/24003692001original/2024 # Cannot find corresponding sequence in NCBI
A/Peregrinefalcon/California/24-005915-001/2024

# These strains represent diversity that's significantly outgrouped relative to cattle outbreak
A/americancrow/Iowa/24006634001/2024
A/Americanwhitepelican/NorthCarolina/W2484/2024
A/baldeagle/Washington/24007953001/2024
A/canadagoose/Indiana/24005146001/2024
A/canadagoose/Indiana/24008719001/2024
A/canadagoose/Missouri/24006385003/2024
A/canadagoose/NewMexico/24005749001/2024
A/Canadagoose/NorthCarolina/W2451/2024
A/Canadagoose/NorthCarolina/W2490A/2024
A/Canadagoose/SouthCarolina/24004559002/2024
A/chicken/California/24000494001original/2024
A/chicken/California/24000494002original/2024
A/chicken/Colorado/24000499001original/2024
A/chicken/Indiana/24005716002/2024
A/chicken/Indiana/24005716003/2024
A/chicken/Indiana/24005716006/2024
A/chicken/Maine/24000724001original/2024
A/chicken/Maine/24000724002original/2024
A/chicken/Maine/24000724003original/2024
A/chicken/Maine/24007946001/2024
A/chicken/Maryland/24005539001/2024
A/chicken/Maryland/24005539002/2024
A/chicken/Minnesota/24000764001original/2024
A/chicken/Minnesota/24005907001/2024
A/chicken/Minnesota/24007263002/2024
A/chicken/Minnesota/24007263003/2024
A/chicken/Ohio/24005334001/2024
A/chicken/Ohio/24005334002/2024
A/chicken/Oregon/24007557001/2024
A/commonraven/California/24007417001/2024
A/crow/Illinois/24004479001/2024
A/crow/Illinois/24004479002/2024
A/domesticcat/Montana/24009038001/2024
A/domesticgoose/California/24000492001original/2024
A/domesticgoose/Minnesota/24000764003original/2024
A/duck/Maine/24004330036/2024
A/duck/Minnesota/24005907002/2024
A/goat/Minnesota/24007234003original/2024
A/goat/Minnesota/24007234006original/2024
A/goat/Minnesota/24007234009/2024
A/goat/Minnesota/24007234029/2024
A/goat/Minnesota/24007234030/2024
A/goat/Minnesota/24007234032/2024
A/goat/Minnesota/24007234034/2024
A/goat/Minnesota/24007234035/2024
A/goat/Minnesota/24007234036/2024
A/goat/Minnesota/24007234037/2024
A/goat/Minnesota/24007234044/2024
A/goat/Minnesota/24007234047/2024
A/goat/Minnesota/24007234048/2024
A/goat/Minnesota/24007234050/2024
A/greathornedowl/Oregon/24006223001/2024
A/hoodedmerganser/SouthCarolina/W24028/2024
A/mallard/Colorado/24003181003/2024
A/mallard/Maine/24004330001/2024
A/mallard/Minnesota/24006961018/2024
A/mallard/NewHampshire/24004334044/2024
A/MountainLion/Montana/01/2024
A/mountainlion/Montana/24005908001/2024
A/mountainlion/Montana/24010315001/2024
A/muteswan/California/24005918001/2024
A/redheadduck/NorthCarolina/W2483A/2024
A/skunk/Montana/24007939001/2024
A/skunk/Washington/24005959001/2024
A/skunk/Washington/24005959002/2024
A/skunk/Washington/24005959003/2024
A/skunk/Washington/24005959004/2024
A/skunk/Washington/24005959005/2024
A/skunk/Washington/24005959006/2024
A/snowgoose/California/24004881002/2024
A/snowgoose/California/24004881004/2024
A/snowgoose/Colorado/24007706001/2024
A/turkey/Minnesota/24007263001/2024
A/turkey/Missouri/24005369001/2024
A/turkey/Missouri/24005369002/2024
A/turkey/Missouri/24005371001/2024
A/turkey/Missouri/24005371002/2024
A/turkey/Missouri/24005372001/2024
A/turkey/Missouri/24005372002/2024
A/turkey/SouthDakota/24007379001/2024
A/turkey/SouthDakota/24007379002/2024
A/turkey/Wisconsin/24000378001original/2024
A/turkey/Wisconsin/24000378002original/2024
A/turkey/Wisconsin/24000378003original/2024
A/turkeyvulture/California/24007419001/2024
A/westerngull/California/24004708001/2024
A/woodduck/Mississippi/24004235001/2024
A/woodduck/NorthCarolina/W24026/2024

A/americancrow/Iowa/24-006634-001/2024
A/Americanwhitepelican/NorthCarolina/W24-84/2024
A/baldeagle/Washington/24-007953-001/2024
A/canada_goose/Indiana/24-005146-001/2024
A/canadagoose/Indiana/24-008719-001/2024
A/canadagoose/Missouri/24-006385-003/2024
A/canadagoose/NewMexico/24-005749-001/2024
A/Canadagoose/NorthCarolina/W24-51/2024
A/Canadagoose/NorthCarolina/W24-90A/2024
A/Canadagoose/SouthCarolina/24004559002/2024 # Cannot find corresponding sequence in NCBI
A/chicken/California/24000494001original/2024 # Cannot find corresponding sequence in NCBI
A/chicken/California/24000494002original/2024 # Cannot find corresponding sequence in NCBI
A/chicken/Colorado/24000499001original/2024 # Cannot find corresponding sequence in NCBI
A/chicken/Indiana/24-005716-002/2024
A/chicken/Indiana/24-005716-003/2024
A/chicken/Indiana/24-005716-006/2024
A/chicken/Maine/24000724001original/2024 # Cannot find corresponding sequence in NCBI
A/chicken/Maine/24000724002original/2024 # Cannot find corresponding sequence in NCBI
A/chicken/Maine/24000724003original/2024 # Cannot find corresponding sequence in NCBI
A/chicken/Maine/24007946001/2024 # Cannot find corresponding sequence in NCBI
A/chicken/Maryland/24-005539-001/2024
A/chicken/Maryland/24-005539-002/2024
A/chicken/Minnesota/24000764001original/2024 # Cannot find corresponding sequence in NCBI
A/chicken/Minnesota/24-005907-001/2024
A/chicken/Minnesota/24-007263-002/2024
A/chicken/Minnesota/24-007263-003/2024
A/chicken/Ohio/24-005334-001/2024
A/chicken/Ohio/24-005334-002/2024
A/chicken/Oregon/24-007557-001/2024
A/commonraven/California/24-007417-001/2024
A/crow/Illinois/24-004479-001/2024
A/crow/Illinois/24-004479-002/2024
A/domesticcat/Montana/24-009038-001/2024
A/domesticgoose/California/24000492001original/2024 # Cannot find corresponding sequence in NCBI
A/domesticgoose/Minnesota/24000764003original/2024 # Cannot find corresponding sequence in NCBI
A/duck/Maine/24004330036/2024 # Cannot find corresponding sequence in NCBI
A/duck/Minnesota/24-005907-002/2024
A/goat/Minnesota/24-007234-003/2024
A/goat/Minnesota/24-007234-006/2024
A/goat/Minnesota/24-007234-009/2024
A/goat/Minnesota/24-007234-029/2024
A/goat/Minnesota/24-007234-030/2024
A/goat/Minnesota/24-007234-032/2024
A/goat/Minnesota/24-007234-034/2024
A/goat/Minnesota/24-007234-035/2024
A/goat/Minnesota/24-007234-036/2024
A/goat/Minnesota/24-007234-037/2024
A/goat/Minnesota/24-007234-044/2024
A/goat/Minnesota/24-007234-047/2024
A/goat/Minnesota/24-007234-048/2024
A/goat/Minnesota/24-007234-050/2024
A/goat/Minnesota/24-007234-059/2024
A/greathornedowl/Oregon/24-006223-001/2024
A/harris-hawk/Utah/24-004080-001/2024
A/hoodedmerganser/SouthCarolina/W24-028/2024
A/mallard/Colorado/24003181003/2024 # Cannot find corresponding sequence in NCBI
A/mallard/Maine/24004330001/2024 # Cannot find corresponding sequence in NCBI
A/mallard/Minnesota/24-006961-018/2024
A/mallard/NewHampshire/24004334044/2024 # Cannot find corresponding sequence in NCBI
A/MountainLion/Montana/01/2024 # Cannot find corresponding sequence in NCBI
A/mountain_lion/Montana/24-005908-001/2024
A/mountain_lion/Montana/24-010315-001/2024
A/muteswan/California/24-005918-001/2024
A/redheadduck/NorthCarolina/W24-83A/2024
A/red-tailedhawk/Oregon/24-008306-001/2024
A/red-tailedhawk/SouthCarolina/24-005993-001/2024
A/skunk/Montana/24-007939-001/2024
A/skunk/Washington/24-005959-001/2024
A/skunk/Washington/24-005959-002/2024
A/skunk/Washington/24-005959-003/2024
A/skunk/Washington/24-005959-004/2024
A/skunk/Washington/24-005959-005/2024
A/skunk/Washington/24-005959-006/2024
A/snow_goose/California/24-004881-002/2024
A/snow_goose/California/24-004881-004/2024
A/snowgoose/Colorado/24-007706-001/2024
A/turkey/Minnesota/24-007263-001/2024
A/turkey/Missouri/24-005369-001/2024
A/turkey/Missouri/24-005369-002/2024
A/turkey/Missouri/24-005371-001/2024
A/turkey/Missouri/24-005371-002/2024
A/turkey/Missouri/24-005372-001/2024
A/turkey/Missouri/24-005372-002/2024
A/turkey/SouthDakota/24-007379-001/2024
A/turkey/SouthDakota/24-007379-002/2024
A/turkey/Wisconsin/24000378001original/2024 # Cannot find corresponding sequence in NCBI
A/turkey/Wisconsin/24000378002original/2024 # Cannot find corresponding sequence in NCBI
A/turkey/Wisconsin/24000378003original/2024 # Cannot find corresponding sequence in NCBI
A/turkeyvulture/California/24-007419-001/2024
A/westerngull/California/24-004708-001/2024
A/woodduck/Mississippi/24004235001/2024 # Cannot find corresponding sequence in NCBI
A/woodduck/NorthCarolina/W24-026/2024
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