From 9f4f69414936ac8ad30e6f03791ba04afefaffc4 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Sun, 20 Nov 2022 10:30:34 +0300 Subject: [PATCH] [build] Update zika build to pull new ingest data Since Ingest pushes data to a different endpoint, update zika build to pull from the new endpoint. Other modifications from the original described below: Since strains (or isolates) may be re-sequenced resulting in duplicate strain names breaking Nextstrain builds, other pathogen repos (e.g. Monkeypox) had switched to indexing records by GenBank ID instead (`rule wrangle_metdata`) and swapping in the final strain name at the end (`rule final_strain_name`) and Zika was updated accordingly. Other changes include updating the list of dropped strain names to GenBank IDs (where the original strain names moved to comments) and updating the example sequence fasta headers. In addition, added the strain name as a Tip Label dropdown item as discussed in: https://github.com/nextstrain/zika/pull/25#discussion_r1117740742 --- Snakefile | 61 ++++++++++--- bin/set_final_strain_name.py | 36 ++++++++ config/auspice_config.json | 5 ++ config/config_zika.yaml | 2 + config/dropped_strains.txt | 167 ++++++++++++++++++----------------- example_data/sequences.fasta | 68 +++++++------- 6 files changed, 211 insertions(+), 128 deletions(-) create mode 100755 bin/set_final_strain_name.py create mode 100644 config/config_zika.yaml diff --git a/Snakefile b/Snakefile index d324ded..56dab5a 100644 --- a/Snakefile +++ b/Snakefile @@ -1,3 +1,6 @@ +if not config: + configfile: "config/config_zika.yaml" + rule all: input: auspice_json = "auspice/zika.json", @@ -17,10 +20,10 @@ rule download: message: "Downloading sequences and metadata from data.nextstrain.org" output: sequences = "data/sequences.fasta.zst", - metadata = "data/metadata.tsv.zst" + metadata = "data/metadata.tsv.zst", params: - sequences_url = "https://data.nextstrain.org/files/zika/sequences.fasta.zst", - metadata_url = "https://data.nextstrain.org/files/zika/metadata.tsv.zst" + sequences_url = "https://data.nextstrain.org/files/workflows/zika/sequences_all.fasta.zst", + metadata_url = "https://data.nextstrain.org/files/workflows/zika/metadata_all.tsv.zst" shell: """ curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences} @@ -30,8 +33,8 @@ rule download: rule decompress: message: "Decompressing sequences and metadata" input: - sequences = "data/sequences.fasta.zst", - metadata = "data/metadata.tsv.zst" + sequences = "data/sequences_all.fasta.zst", + metadata = "data/metadata_all.tsv.zst" output: sequences = "data/sequences.fasta", metadata = "data/metadata.tsv" @@ -41,6 +44,20 @@ rule decompress: zstd -d -c {input.metadata} > {output.metadata} """ +rule wrangle_metadata: + input: + metadata="data/metadata.tsv" + output: + metadata="results/wrangled_metadata.tsv", + params: + strain_id=lambda w: config.get("strain_id_field", "strain"), + shell: + """ + csvtk -t rename -f strain -n strain_original {input.metadata} \ + | csvtk -t mutate -f {params.strain_id} -n strain > {output.metadata} + """ + + rule filter: message: """ @@ -51,8 +68,8 @@ rule filter: - minimum genome length of {params.min_length} (50% of Zika virus genome) """ input: - sequences = rules.decompress.output.sequences, - metadata = rules.decompress.output.metadata, + sequences = "data/sequences.fasta", + metadata = rules.wrangle_metadata.output.metadata, exclude = files.dropped_strains output: sequences = "results/filtered.fasta" @@ -120,7 +137,7 @@ rule refine: input: tree = rules.tree.output.tree, alignment = rules.align.output, - metadata = rules.decompress.output.metadata + metadata = rules.wrangle_metadata.output.metadata output: tree = "results/tree.nwk", node_data = "results/branch_lengths.json" @@ -186,7 +203,7 @@ rule traits: """ input: tree = rules.refine.output.tree, - metadata = rules.decompress.output.metadata + metadata = rules.wrangle_metadata.output.metadata output: node_data = "results/traits.json", params: @@ -207,7 +224,7 @@ rule export: message: "Exporting data files for for auspice" input: tree = rules.refine.output.tree, - metadata = rules.decompress.output.metadata, + metadata = rules.wrangle_metadata.output.metadata, branch_lengths = rules.refine.output.node_data, traits = rules.traits.output.node_data, nt_muts = rules.ancestral.output.node_data, @@ -216,7 +233,8 @@ rule export: auspice_config = files.auspice_config, description = files.description output: - auspice_json = rules.all.input.auspice_json + auspice_json = "results/raw_zika.json", + root_sequence = "results/raw_zika_root-sequence.json", shell: """ augur export v2 \ @@ -230,6 +248,27 @@ rule export: --output {output.auspice_json} """ +rule final_strain_name: + input: + auspice_json=rules.export.output.auspice_json, + metadata=rules.wrangle_metadata.output.metadata, + root_sequence=rules.export.output.root_sequence, + output: + auspice_json=rules.all.input.auspice_json, + root_sequence="auspice/zika_root-sequence.json", + params: + display_strain_field=lambda w: config.get("display_strain_field", "strain"), + shell: + """ + python3 bin/set_final_strain_name.py \ + --metadata {input.metadata} \ + --input-auspice-json {input.auspice_json} \ + --display-strain-name {params.display_strain_field} \ + --output {output.auspice_json} + + cp {input.root_sequence} {output.root_sequence} + """ + rule clean: message: "Removing directories: {params}" params: diff --git a/bin/set_final_strain_name.py b/bin/set_final_strain_name.py new file mode 100755 index 0000000..0036f2a --- /dev/null +++ b/bin/set_final_strain_name.py @@ -0,0 +1,36 @@ +import pandas as pd +import json, argparse + +def replace_name_recursive(node, lookup): + if node["name"] in lookup: + node["name"] = lookup[node["name"]] + + if "children" in node: + for child in node["children"]: + replace_name_recursive(child, lookup) + +if __name__=="__main__": + parser = argparse.ArgumentParser( + description="Swaps out the strain names in the Auspice JSON with the final strain name", + formatter_class=argparse.ArgumentDefaultsHelpFormatter + ) + + parser.add_argument('--input-auspice-json', type=str, required=True, help="input auspice_json") + parser.add_argument('--metadata', type=str, required=True, help="input data") + parser.add_argument('--display-strain-name', type=str, required=True, help="field to use as strain name in auspice") + parser.add_argument('--output', type=str, metavar="JSON", required=True, help="output Auspice JSON") + args = parser.parse_args() + + metadata = pd.read_csv(args.metadata, sep='\t') + name_lookup = {} + for ri, row in metadata.iterrows(): + strain_id = row['strain'] + name_lookup[strain_id] = args.display_strain_name if pd.isna(row[args.display_strain_name]) else row[args.display_strain_name] + + with open(args.input_auspice_json, 'r') as fh: + data = json.load(fh) + + replace_name_recursive(data['tree'], name_lookup) + + with open(args.output, 'w') as fh: + json.dump(data, fh) diff --git a/config/auspice_config.json b/config/auspice_config.json index b3ba0c8..be302f4 100644 --- a/config/auspice_config.json +++ b/config/auspice_config.json @@ -5,6 +5,11 @@ ], "build_url": "https://github.com/nextstrain/zika", "colorings": [ + { + "key": "strain_original", + "title": "strain name", + "type": "categorical" + }, { "key": "gt", "title": "genotype", diff --git a/config/config_zika.yaml b/config/config_zika.yaml new file mode 100644 index 0000000..aa8d020 --- /dev/null +++ b/config/config_zika.yaml @@ -0,0 +1,2 @@ +strain_id_field: "accession" +display_strain_field: "strain_original" \ No newline at end of file diff --git a/config/dropped_strains.txt b/config/dropped_strains.txt index 22b5878..746e1ba 100644 --- a/config/dropped_strains.txt +++ b/config/dropped_strains.txt @@ -1,86 +1,87 @@ -PF13/251013_18 # reference included in config/zika_reference.gb -AFMC_U # too basal -AFMC_S # too basal -Boracay/16423 # too basal -JMB_185 # too basal -PHL/2012/CPC_0740 # too basal +MG827392 +KX369547 # PF13/251013_18 # reference included in config/zika_reference.gb +KY553111 # AFMC_U # too basal +KY962729 # AFMC_S # too basal +KY120353 # Boracay/16423 # too basal +KU179098 # JMB_185 # too basal +KU681082 # PHL/2012/CPC_0740 # too basal VIE/Bra/2016 # too basal -Dominican_Republic/2016/PD2 # duplicate of other strain in dataset -GD01 # duplicate of other strain in dataset -GDZ16001 # duplicate of other strain in dataset -VEN/UF_2/2016 # duplicate of other strain in dataset -ZZ_1 # duplicate of other strain in dataset -VR10599/Pavia/2016 # export with unknown origin -34997/Pavia/2016 # export with unknown origin -COL/FLR_00001/2015 # duplicate of COL/FLR/2015 -COL/FLR_00002/2015 # duplicate of COL/FLR/2015 -COL/FLR_00003/2015 # duplicate of COL/FLR/2015 -COL/FLR_00004/2015 # duplicate of COL/FLR/2015 -COL/FLR_00005/2015 # duplicate of COL/FLR/2015 -COL/FLR_00006/2015 # duplicate of COL/FLR/2015 -COL/FLR_00007/2015 # duplicate of COL/FLR/2015 -COL/FLR_00008/2015 # duplicate of COL/FLR/2015 -COL/FLR_00009/2015 # duplicate of COL/FLR/2015 -COL/FLR_00010/2015 # duplicate of COL/FLR/2015 -COL/FLR_00011/2015 # duplicate of COL/FLR/2015 -COL/FLR_00012/2015 # duplicate of COL/FLR/2015 -COL/FLR_00013/2015 # duplicate of COL/FLR/2015 -COL/FLR_00014/2015 # duplicate of COL/FLR/2015 -COL/FLR_00015/2015 # duplicate of COL/FLR/2015 -COL/FLR_00016/2015 # duplicate of COL/FLR/2015 -COL/FLR_00017/2015 # duplicate of COL/FLR/2015 -COL/FLR_00018/2015 # duplicate of COL/FLR/2015 -COL/FLR_00019/2015 # duplicate of COL/FLR/2015 -COL/FLR_00020/2015 # duplicate of COL/FLR/2015 -COL/FLR_00021/2015 # duplicate of COL/FLR/2015 -COL/FLR_00022/2015 # duplicate of COL/FLR/2015 -COL/FLR_00023/2015 # duplicate of COL/FLR/2015 -COL/FLR_00024/2015 # duplicate of COL/FLR/2015 -COL/FLR_00025/2015 # duplicate of COL/FLR/2015 -COL/FLR_00026/2015 # duplicate of COL/FLR/2015 -COL/FLR_00034/2015 # duplicate of COL/FLR/2015 -COL/FLR_00035/2015 # duplicate of COL/FLR/2015 -COL/FLR_00036/2015 # duplicate of COL/FLR/2015 -COL/FLR_00038/2015 # duplicate of COL/FLR/2015 -COL/FLR_00040/2015 # duplicate of COL/FLR/2015 -COL/FLR_00041/2015 # duplicate of COL/FLR/2015 -COL/FLR_00042/2015 # duplicate of COL/FLR/2015 -COL/PRV_00027/2015 # misdated -COL/PRV_00028/2015 # misdated -COL/PAN_00029/2015 # misdated -COL/PAN_00030/2015 # misdated -BRA/2016/FC_DQ12D1 # large indel -Brazil/2016/ZBRX8 # large indel -Brazil/2016/ZBRX11 # large indel -CX17 # large indel -MEX/2016/mex27 # large indel -MEX/2016/mex50 # large indel -SLV/2016/ElSalvador_1055 # large indel -USVI/20/2016 # large indel +KU853013 # Dominican_Republic/2016/PD2 # duplicate of other strain in dataset +KU740184 # GD01 # duplicate of other strain in dataset +KU761564 # GDZ16001 # duplicate of other strain in dataset +KX893855 # VEN/UF_2/2016 # duplicate of other strain in dataset +KY927808 # ZZ_1 # duplicate of other strain in dataset +KY003154 # VR10599/Pavia/2016 # export with unknown origin +KY003153 # 34997/Pavia/2016 # export with unknown origin +MF574552 # COL/FLR_00001/2015 # duplicate of COL/FLR/2015 +MF574559 # COL/FLR_00002/2015 # duplicate of COL/FLR/2015 +MF574560 # COL/FLR_00003/2015 # duplicate of COL/FLR/2015 +MF574561 # COL/FLR_00004/2015 # duplicate of COL/FLR/2015 +MF574571 # COL/FLR_00005/2015 # duplicate of COL/FLR/2015 +MF574555 # COL/FLR_00006/2015 # duplicate of COL/FLR/2015 +MF574557 # COL/FLR_00007/2015 # duplicate of COL/FLR/2015 +MF574562 # COL/FLR_00008/2015 # duplicate of COL/FLR/2015 +MF574572 # COL/FLR_00009/2015 # duplicate of COL/FLR/2015 +MF574570 # COL/FLR_00010/2015 # duplicate of COL/FLR/2015 +MF574565 # COL/FLR_00011/2015 # duplicate of COL/FLR/2015 +MF574568 # COL/FLR_00012/2015 # duplicate of COL/FLR/2015 +MF574558 # COL/FLR_00013/2015 # duplicate of COL/FLR/2015 +MF574576 # COL/FLR_00014/2015 # duplicate of COL/FLR/2015 +MF574567 # COL/FLR_00015/2015 # duplicate of COL/FLR/2015 +MF574575 # COL/FLR_00016/2015 # duplicate of COL/FLR/2015 +MF574553 # COL/FLR_00017/2015 # duplicate of COL/FLR/2015 +MF574573 # COL/FLR_00018/2015 # duplicate of COL/FLR/2015 +MF574574 # COL/FLR_00019/2015 # duplicate of COL/FLR/2015 +MF574577 # COL/FLR_00020/2015 # duplicate of COL/FLR/2015 +MF574556 # COL/FLR_00021/2015 # duplicate of COL/FLR/2015 +MF574554 # COL/FLR_00022/2015 # duplicate of COL/FLR/2015 +MF574566 # COL/FLR_00023/2015 # duplicate of COL/FLR/2015 +MF574569 # COL/FLR_00024/2015 # duplicate of COL/FLR/2015 +MF574563 # COL/FLR_00025/2015 # duplicate of COL/FLR/2015 +MF574564 # COL/FLR_00026/2015 # duplicate of COL/FLR/2015 +MF574581 # COL/FLR_00034/2015 # duplicate of COL/FLR/2015 +MF574588 # COL/FLR_00035/2015 # duplicate of COL/FLR/2015 +MF574582 # COL/FLR_00036/2015 # duplicate of COL/FLR/2015 +MF574586 # COL/FLR_00038/2015 # duplicate of COL/FLR/2015 +MF574584 # COL/FLR_00040/2015 # duplicate of COL/FLR/2015 +MF574583 # COL/FLR_00041/2015 # duplicate of COL/FLR/2015 +MF574580 # COL/FLR_00042/2015 # duplicate of COL/FLR/2015 +MF574579 # COL/PRV_00027/2015 # misdated +MF574578 # COL/PRV_00028/2015 # misdated +MF574585 # COL/PAN_00029/2015 # misdated +MF574587 # COL/PAN_00030/2015 # misdated +KY785436 # BRA/2016/FC_DQ12D1 # large indel +KY559010 # Brazil/2016/ZBRX8 # large indel +KY559011 # Brazil/2016/ZBRX11 # large indel +KX986761 # CX17 # large indel +MF801405 # MEX/2016/mex27 # large indel +MF801424 # MEX/2016/mex50 # large indel +MF801377 # SLV/2016/ElSalvador_1055 # large indel +VI20_12plex # USVI/20/2016 # large indel USVI/21/2016 # large indel -USVI/23/2016 # large indel -USVI/27/2016 # large indel -USVI/30/2016 # large indel -USVI/32/2016 # large indel -Thailand/1605aTw # excess divergence -VE_Ganxian # excess divergence -ZK_YN001 # excess divergence -Haiti/0029/2014 # contamination present -Haiti/0033/2014 # contamination present -Haiti/0036/2014 # contamination present -Haiti/0054/2014 # contamination present -Haiti/0074/2014 # contamination present -Haiti/0097/2014 # contamination present -mosquito/Haiti/1682/2016 # contamination present +VI23_12plex # USVI/23/2016 # large indel +VI27_1d # USVI/27/2016 # large indel +VI30_1d # USVI/30/2016 # large indel +VI32_12plex # USVI/32/2016 # large indel +KY126351 # Thailand/1605aTw # excess divergence +KU744693 # VE_Ganxian # excess divergence +KY328290 # ZK_YN001 # excess divergence +KY415986 # Haiti/0029/2014 # contamination present +KY415987 # Haiti/0033/2014 # contamination present +KY415990 # Haiti/0036/2014 # contamination present +KY415988 # Haiti/0054/2014 # contamination present +KY415989 # Haiti/0074/2014 # contamination present +KY415991 # Haiti/0097/2014 # contamination present +MF384325 # mosquito/Haiti/1682/2016 # contamination present ZF36_36S # contamination present -MR766 # lab strain -Aedes_sp/MEX_I_44/2016 # duplicate of Aedes_aegypti/MEX/MEX_I_44/2016 -Puerto_Rico/2015/PRVABC59 # duplicate of PRVABC59 -V15555 # highly diverged -DK # lab strain -DK23 # lab strain -rGZ02a/2018 # highly diverged -rGZ02p/2018 # highly diverged -V211784 # highly diverged -LMM/AG5643 -Faranah/18 +MK105975 # MR766 # lab strain +KX856011 # Aedes_sp/MEX_I_44/2016 # duplicate of Aedes_aegypti/MEX/MEX_I_44/2016 +MK028857 # Puerto_Rico/2015/PRVABC59 # duplicate of PRVABC59 +MN025403 # V15555 # highly diverged +MT505349 # DK # lab strain +MT505350 # DK23 # lab strain +MW680969 # rGZ02a/2018 # highly diverged +MW680970 # rGZ02p/2018 # highly diverged +OK054351 # V211784 # highly diverged +MT478034 # LMM/AG5643 +OL414716 # Faranah/18 diff --git a/example_data/sequences.fasta b/example_data/sequences.fasta index 64facba..9203c90 100644 --- a/example_data/sequences.fasta +++ b/example_data/sequences.fasta @@ -1,4 +1,4 @@ ->PAN/CDC_259359_V1_V3/2015 +>KX156774 gaatttgaagcgaatgctaacaacagtatcaacaggttttattttggatttggaaacgag agtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgc taaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggac @@ -179,7 +179,7 @@ gaccttccccacccttcaatctggggcctgaactggagatcagctgtggatctccagaag agggactagtggttagaggagaccccccggaaaacgcaaaacagcatattgacgctggga aagaccagagactccatgagtttccaccacgctggccgccaggcacagatcgccgaatag cggcggccggtgtggggaaatccatgggtct ->COL/FLR_00024/2015 +>MF574569 tcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttatt ttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggatt ccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaa @@ -358,7 +358,7 @@ agctgggaaaccaagcctatagtcaggccgagaacgccatggcacggaagaagccatgct gcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcagga tgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagatcag ctgtggatctccagaagagggactagtggttagaggaga ->PRVABC59 +>KU501215 gttgttgatctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaaca gtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaaa aaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtgag @@ -537,7 +537,7 @@ tgtgacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatgg cacggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaaccccac gcgcttggaggcgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctggg gcctgaactggagatcagctgtggatctccagaagagggactagtggttagagga ->COL/FLR_00008/2015 +>MF574562 tcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttatt ttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggatt ccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaa @@ -716,7 +716,7 @@ agctgggaaaccaagcctatagtcaggccgagaacgccatggcacggaagaagccatgct gcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcagga tgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagatcag ctgtggatctccagaagagggactagtggttagaggaga ->Colombia/2016/ZC204Se +>KY317939 gacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttg gaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgt caatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgcc @@ -894,7 +894,7 @@ agtcagccacagcttggggaaagctgtgcagcctgtgacccccccaggagaagctgggaa accaagcctatagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgag cccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaag aaggtggcgaccttccccacccttcaatctggggcctgaactggagat ->ZKC2/2016 +>KX253996 agttgttgatctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaac agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga @@ -1076,7 +1076,7 @@ ggcctgaactggagatcagctgtggatctccagaagagggactagtggttagaggagacc ccccggaaaacgcaaaacagcatattgacgctgggaaagaccagagactccatgagtttc caccacgctggccgccaggcacagatcgccgaatagcggcggccggtgtggggaaatcca tgggtct ->VEN/UF_1/2016 +>KX702400 agttgttactgttgctgactcagactgcgacagttcgagtttgaagcgaaagctagcaac agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga @@ -1258,7 +1258,7 @@ ggcctgaactggagatcagctgtggatctccagaagagggactagtggttagaggagacc ccccggaaaacgcaaaacagcatattgacgctgggaaagaccagagactccatgagtttc caccacgctggccgccaggcacagatcgccgaatagcggcggccggtgtggggaaatcca tgggtctt ->DOM/2016/BB_0059 +>KY785425 tggctgccatgctgagaataatcaatgctaggaaggagaagaagagacgaggcgcagata ctagtgtcggaattgttggcctcctgctgaccacagctatggcagcggaggtcactagac gtgggagtgcatactacatgtacttggacagaaacgatgctggggaggccatatctttcc @@ -1427,7 +1427,7 @@ ggtgtggatctctcatagggcacagaccgcgcaccacctgggctgagaacattaaaaaca cagtcaacatggtgcgcaggatcataggtgaggaagaaaagtacatggactacctatcca cccaagttcgctacttgggtgaagaagggtctacacctggagtgctgtaagcaccaatct taatgttgtcaggcc ->BRA/2016/FC_6706 +>KY785433 agtttgaagcgaaagctagcaacagtatcaacaggttttatttyggatttggaaacgaga gtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgct aaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggact @@ -1601,7 +1601,7 @@ cattccctatttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagacc gcgcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcatagg tgatgaagaaaagtacatggactacctatccacccaagttcgctacttgggtgaagaagg gtctacacctggagtgctgtaagcaccaatcttaatgttgtcaggc ->DOM/2016/BB_0183 +>KY785420 gtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagag tttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgcta aaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggactt @@ -1780,7 +1780,7 @@ tagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctcagag gacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcga ccttccccacccttcaatctggggcctgaactggagatcagctgtggatccccagaagag g ->EcEs062_16 +>KX879603 agtagttgatctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaac agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga @@ -1962,7 +1962,7 @@ ggcctgaactggagatcagctgtggatctccagaagagggactagtggttagaggagacc ccccggaaaacgcaaaacagcatattgacgctgggaaagaccagagactccatgagtttc caccacgctggccgccaggcacagatcgccgaatagcggcggccggtgtggggaaatcca tgggagatcgga ->HND/2016/HU_ME59 +>KY785418 gtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagag tttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgcta aaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggactt @@ -2136,7 +2136,7 @@ attccctatttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagaccg cgcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcataggt gatgaagaaaagtacatggactacctatccacccaagttcgctacttgggtgaagaaggg tctacacctggagtgctgtaagcaccaatcttaatgttgtcaggc ->DOM/2016/MA_WGS16_011 +>KY785484 aagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagagtttct ggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaaaacg cggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttctgct @@ -2314,7 +2314,7 @@ ggggaaagctgtgcagcctgtgacccccccaggagaagctgggaaaccaagcctatagtc aggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctcagaggacac tgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttc cccacccttcaatctggggcctgaactggggatcag ->DOM/2016/BB_0433 +>KY785441 tttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagagt ttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaa aacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttc @@ -2488,7 +2488,7 @@ ttccctatttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagaccgc gcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcataggtg aggaagaaaagtacatggactacctatccacccaagttcgctacttgggtgaagaagggt ctacacctggagtgctgtaagcaccaatcctaatgttgtcaggcc ->USA/2016/FL022 +>KY075935 gcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatt tggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggatt gtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctg @@ -2662,7 +2662,7 @@ aaatggacagacattccctatttgggaaaaagggaagacttgtggtgtggatctctcata gggcacagaccgcgcaccacctgggctgagaacattaaaaacacagtcaacatggtgcgc aggatcataggtgaggaagaaaagtacatggactacctatccacccaagtccgctacttg ggtgaagaagggtctacacctggagtgctgtaagcaccaatctta ->SG_027 +>KY241697 ctgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttgga tttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccgga ttgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggc @@ -2842,7 +2842,7 @@ tgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatggga aaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagatcagctgtg gatctccagaagagggactagtggttagaggagaccccccggaaaacgcaaaacagcata ttgacgctgggaaagaccagagactccatgagtttccaccacgctggccgccag ->SG_074 +>KY241744 gaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggtttt attttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggagg attccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggctt @@ -3023,7 +3023,7 @@ ggatgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagat cagctgtggatctccagaagagggactagtggttagaggagaccccccggaaaacgcaaa acagcatattgacgctgggaaagaccagagactccatgagtttccaccacgctggccgcc aggcacagatcgccgaatagcg ->SG_056 +>KY241726 gaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggtttt attttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggagg attccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggctt @@ -3203,7 +3203,7 @@ gctgcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgca ggatgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactggagat cagctgtggatctccagaagagggactagtggttagaggagaccccccggaaaacgcaaa acagcatattgacgctgggaaagaccagagactccatgagtttccaccacgctggcc ->USA/2016/FLUR022 +>KY325473 gtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacagg ttttattttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccg gaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggg @@ -3384,7 +3384,7 @@ cgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctggggcctgaactgg agatcagctgtggatctccagaagagggactagtggttagaggagaccccccggaaaacg caaaacagcatattgacgctgggaaagaccagagactccatgagtttccaccacgctggc cgccaggcacagatcgccgaatagcggcggccggtgtggggaaatc ->Aedes_aegypti/USA/2016/FL05 +>KY075937 gacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttg gaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgt caatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgcc @@ -3562,7 +3562,7 @@ agtcagccacagcttggggaaagctgtgcagcctgtgacccccccaggagaagctgggaa accaagcctatagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgag cccctcagaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaag aaggtggcgaccttccccacccttcaatctggggcctgaactggagat ->SG_018 +>KY241688 atgnnnnnnnnnnnnnnnnnnnccggaggattccggattgtcaatatgctaaaacgcgga gtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttctgctgggt catgggcccatcaggatggtcttggcgattctagcctttttgaggttcacggcaatcaag @@ -3741,7 +3741,7 @@ tcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttcccca cccttcaatctggggcctgaactggagatcagctgtggatctccagaagagggactagtg gttagaggagaccccccggaaaacgcaaaacagcatattgacgctgggaaagaccagaga ctccatgagtttccaccacgctggccgccaggcacagat ->USA/2016/FLWB042 +>KY325478 ctttgggggcttgaagaggctgccagccggacttctgctgggtcatgggcccatcaggat ggtcttggcgattctagcctttttgagattcacggcaatcaagccatcactgggtctcat caatagatggggttcagtggggaaaaaagaggctatggaaataataaagaagttcaagaa @@ -3916,7 +3916,7 @@ aatctcaatgttgtcaggcctgctagtcagccacagcttggggaaagctgtgcagcctgt gacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatggcac ggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaaccccacgcg cttggaggcgcaggnnnnnnaaagaag ->COL/PRV_00028/2015 +>MF574578 ttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacgagagtt tctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaaa acgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttct @@ -4095,7 +4095,7 @@ gtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctcagagga cactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtggcgacc ttccccacccttcaatctggggcctgaactggagatcagctgtggatctccagaagaggg actagtggttagaggaga ->Thailand/1610acTw +>MF692778 gcaacagtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaa cccaaaaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccg tgtgagcccctttgggggcttgaagaggctgccagccggacttctgctgggccatgggcc @@ -4271,7 +4271,7 @@ ggactacctatccacccaagttcgctacttgggtgaagaagggtctacacctggagtgct gtaagcaccaatcttagtgttgtcaggcctgctagtcagccacagcttggggaaagctgt gcagcctgtgacccccccaggagaagctgggaaaccaagcccatagtcaggccgagaacg ccatggcacggaag ->1_0087_PF +>KX447509 agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga gcccctttgggggcttgaagaggctgccagccggacttctgctgggtcatgggcccatca @@ -4449,7 +4449,7 @@ ctgtgacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatg gcacggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaacccca cgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctgg ggcctgaactggagatcagctgtggat ->1_0199_PF +>KX447519 actgcgacagttcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttgg atttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccgg attgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagagg @@ -4603,7 +4603,7 @@ tgggctctagtggacaaggaaagagagcaccacctgagaggagagtgccagagttgtgtg tacaacatgatgggaaaaagagaaaagaaacaaggggaatttggaaaggccaagggcagc cgcgccatctggtatatgtggctaggggctagatttctagagttcgaagcccttggattc ttgaacgaggatcactggatgg ->1_0181_PF +>KX447512 agtatcaacaggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaa aaaagaaatccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtga gcccctttgggggcttgaagaggctgccagccggacttctgctgggtcatgggcccatca @@ -4781,7 +4781,7 @@ ctgtgacccccccaggagaagctgggaaaccaagcctatagtcaggccgagaacgccatg gcacggaagaagccatgctgcctgtgagcccctcagaggacactgagtcaaaaaacccca cgcgcttggaggcgcaggatgggaaaagaaggtggcgaccttccccacccttcaatctgg ggcctgaactggagatcagctgtgga ->Brazil/2015/ZBRC301 +>KY558995 gatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccg gattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagag gctgccagccggacttctgctgggtcatgggcccatcaggatggtcttggcgattctagc @@ -4950,7 +4950,7 @@ gactgcttgcctagcaaaatcatatgcgcagatgtggcagctcctttatttccacagaan ggacctccgactgatggccaatgccatttgttcatctgtgccagttgactgggttccaac tgggagaactacctggtcaatccatggaaanggagaatggatgaccactgaagacatgct tg ->Brazil/2015/ZBRA105 +>KY558989 gatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccg gattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagag gctgccagccggacttctgctgggtcatgggcccatcaggatggtcttggcgattctagc @@ -5119,7 +5119,7 @@ gactgcttgcctagcaaaatcatatgcgcaaatgtggcagctcctttatttccacagaag ggacctccgactgatggccaatgccatttgttcatctgtgccagttgactgggttccaac tgggagaactacctggtcaatccatggaaagggagaatggatgaccactgaagacatgct tg ->Brazil/2016/ZBRC16 +>KY558991 tgagaataatcaatgctaggaaggagaagaagagacgaggcgcagatactagtgtcggaa ttgttggcctcctgctgaccacagctatggcagcggaggtcactagacgtgggagtgcat actatatgtacttggacagaaacgatgctggggaggccatatcttttccaaccacattgg @@ -5272,7 +5272,7 @@ atgcagatgacactgctggctgggacacccgcatcagcaggtttgatctggagaatgaag ctctaatcaccaaccaaatggagagagggcacagggccttggcattggccataatcaagt acacataccaaaacaaagtggtaaaggtccttagaccagctgaaaaagggaaaacagtta tggacatcatttcgagacaagaccaaaggggg ->V8375 +>KU501217 atgaaaaacccaaaaaagaaatccggaggattccggattgtcaatatgctaaaacgcgga gtagcccgtgtgagcccctttgggggcttgaagaggctgccagccggacttctgctgggt catgggcccatcaggatggtcttggcgattctagcctttttgagattcacggcaatcaag @@ -5445,7 +5445,7 @@ ttgggaaaaagggaagacttgtggtgtggatctctcatagggcacagaccgcgcaccacc tgggctgagaacattaaaaacacagtcaacatggtgcgcaggatcataggtgatgaagaa aagtacatggactacctatccacccaagttcgctacttgggtgaagaagggtctacacct ggagtgctgtaa ->Nica1_16 +>KX421195 tcgagtttgaagcgaaagctagcaacagtatcaacaggttttattttggatttggaaacg agagtttctggtcatgaaaaacccaaaaaagaaatccggaggattccggattgtcaatat gctaaaacgcggagtagcccgtgtgagcccctttgggggcttgaagaggctgccagccgg @@ -5624,7 +5624,7 @@ cctatagtcaggccgagaacgccatggcacggaagaagccatgctgcctgtgagcccctc agaggacactgagtcaaaaaaccccacgcgcttggaggcgcaggatgggaaaagaaggtg gcgaccttccccacccttcaatctggggcctgaactggagatcagctgtggatctccaga agagggactagtggttagaggag ->Brazil/2015/ZBRC303 +>KY558997 tgagaataatcaatgctaggaaggagaagaagagacgaggcacagatactagtgtcggaa ttgttggcctcctgctgaccacagctatggcagcggaggtcactagacgtgggagtgcat actatatgtacttggacagaaacgatgctggggaggccatatcttttccaaccacattgg @@ -5782,7 +5782,7 @@ agatgcaagacttgtggctgctgcggaggtcagagaaagtgaccaactggttgcagagca acggatgggataggctcaaacgaatggcagtcagtggagatgattgcgttgtgaagccaa ttgatgataggtttgcacatgccctcaggttcttgaatgatatgggaaaagttaggaagg acacacaagagtgg ->SMGC_1 +>KX266255 tctgtgtgaatcagactgcgacagttcgagtttgaagcgaaagctagcaacagtatcaac aggttttattttggatttggaaacgagagtttctggtcatgaaaaacccaaaaaagaaat ccggaggattccggattgtcaatatgctaaaacgcggagtagcccgtgtgagcccctttg