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contaminome.yml
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contaminome.yml
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eukaryotes:
Homo Sapiens:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.fna.gz
vulgarname: human
accession: GCF_000001405.40
taxid: 9606
Mus musculus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.27_GRCm39/GCF_000001635.27_GRCm39_genomic.fna.gz
vulgarname: mouse
accession: GCF_000001635.27
taxid: 10090
Drosophila melanogaster:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.gz
vulgarname: fly
accession: GCF_000001215.4
taxid: 7227
Aedes aegypti:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/204/515/GCF_002204515.2_AaegL5.0/GCF_002204515.2_AaegL5.0_genomic.fna.gz
vulgarname: aedes-aegypti
accession: GCF_002204515.2
taxid: 7159
Petromyzon marinus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/993/605/GCF_010993605.1_kPetMar1.pri/GCF_010993605.1_kPetMar1.pri_genomic.fna.gz
vulgarname: sea-lamprey
accession: GCF_010993605.1
taxid: 7757
Oryzias latipes:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/234/675/GCF_002234675.1_ASM223467v1/GCF_002234675.1_ASM223467v1_genomic.fna.gz
vulgarname: japanese-medaka
accession: GCF_002234675.1
taxid: 8090
Caenorhabditis elegans:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/GCF_000002985.6_WBcel235_genomic.fna.gz
vulgarname: c-elegans
accession: GCF_000002985.6
taxid: 6239
Saccharomyces cerevisiae:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_genomic.fna.gz
vulgarname: yeast
accession: GCF_000146045.2
taxid: 4932
Danio rerio:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.6_GRCz11/GCF_000002035.6_GRCz11_genomic.fna.gz
vulgarname: zebrafish
accession: GCF_000002035.6
taxid: 7955
Hypsibius dujardini:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/579/985/GCA_001579985.1_ASM157998v1/GCA_001579985.1_ASM157998v1_genomic.fna.gz
vulgarname: moss-piglet
accession: GCA_001579985.1
taxid: 232323
prokaryotes:
Escherichia coli:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
vulgarname: ecoli
accession: GCF_000005845.2
taxid: 562
Pseudomonas aeruginosa:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/765/GCF_000006765.1_ASM676v1/GCF_000006765.1_ASM676v1_genomic.fna.gz
vulgarname: pseudomonas-aeruginosa
accession: GCF_000006765.1
taxid: 287
Pseudomonas putidia:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/412/675/GCF_000412675.1_ASM41267v1/GCF_000412675.1_ASM41267v1_genomic.fna.gz
vulgarname: pseudomonas-putidia
accession: GCF_000412675.1
taxid: 1211579
Pseudomonas fulva:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/186/195/GCF_001186195.1_ASM118619v1/GCF_001186195.1_ASM118619v1_genomic.fna.gz
vulgarname: pseudomonas-fulva
accession: GCF_001186195.1
taxid: 47880
Acholeplasma laidlawii:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/385/765/GCF_003385765.1_ASM338576v1/GCF_003385765.1_ASM338576v1_genomic.fna.gz
vulgarname: mycoplasma
accession: GCF_003385765.1
taxid: 2148
Mesomycoplasma hyorhinis:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/383/515/GCF_000383515.1_ASM38351v1/GCF_000383515.1_ASM38351v1_genomic.fna.gz
vulgarname: mycoplasma-hyorhinis
accession: GCF000383515.1
taxid: 2100
Haemophilus influenzae:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/931/575/GCF_000931575.1_ASM93157v1/GCF_000931575.1_ASM93157v1_genomic.fna.gz
vulgarname: haemophilus
accession: GCF_000931575.1
taxid: 727
Wolbachia melanogaster symbiont:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/584/425/GCA_016584425.1_ASM1658442v1/GCA_016584425.1_ASM1658442v1_genomic.fna.gz
vulgarname: wolbachia
accession: GCF_016584425.1
taxid: 163164
Staphylococcus aureus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/425/GCF_000013425.1_ASM1342v1/GCF_000013425.1_ASM1342v1_genomic.fna.gz
vulgarname: staph_aureus
accession: GCF_000013425.1
taxid: 1280
custom:
Severe acute respiratory syndrome coronavirus 2:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz
vulgarname: sars-cov2
accession: GCF_009858895.2
taxid: 2697049
Influenza A:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/865/085/GCF_000865085.1_ViralMultiSegProj15622/GCF_000865085.1_ViralMultiSegProj15622_genomic.fna.gz
vulgarname: flu-a
accession: GCF_000865085.1
taxid: 335341
Norwalk virus:
URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/864/005/GCF_000864005.1_ViralProj15520/GCF_000864005.1_ViralProj15520_genomic.fna.gz
vulgarname: noro
accession: GCF_000864005.1
taxid: 11983
Influenza B:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/influenzab.fna.gz
vulgarname: flu-b
accession: NC_002211.1
taxid: 11520
Rhinovirus A:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/rhinoa.fna.gz
vulgarname: common-cold-a
accession: NC_038311.1
taxid: 573824
Rhinovirus B:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/rhinob.fna.gz
vulgarname: common-cold-b
accession: NC_001490.1
taxid: 12131
Drosophila C virus:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/drosophilac.fna.gz
vulgarname: drosophila-c-virus
accession: NC_001834.1
taxid: 64279
Escherichia phage phiX174:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/phix.fna.gz
vulgarname: phix
accession: NC_001422.1
taxid: 2886930
Enterobacteria phage lambda:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/lambdaphage.fna.gz
vulgarname: lambdaphage
accession: NC_001416.1
taxid: 10710
UniVec_core:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/univec_core.fna.gz
vulgarname: vectors
accession: NA
taxid: 29278
ERCC:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/ercc.fna.gz
vulgarname: ercc
accession: NA
taxid: 292781111
rrna:
Homo sapiens pre-rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/human45s.fna.gz
vulgarname: humanrrna
accession: NR_046235.3
taxid: 96061111
Mus musculus pre-rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/mouse45s.fna.gz
vulgarname: mouserrna
accession: NR_046233.2
taxid: 100901111
Drosophila melanogaster pre-rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/fly45s.fna.gz
vulgarname: flyrrna
accession: NR_133549.1
taxid: 72271111
Aedes aegypti 28SrRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/aedesaegypti28s.fna.gz
vulgarname: aedesaegyptirrna
accession: NC_035159.1
taxid: 71591111
Zebrafish rRNA:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/zebrarRNA.fna.gz
vulgarname: zebrafishrrna
accession: NR_145818.1
taxid: 79551111
mito:
Homo sapiens mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/humanmito.fna.gz
vulgarname: humanmito
accession: NC_012920.1
taxid: 96062222
Mus musculus mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/mousemito.fna.gz
vulgarname: mousemito
accession: NC_005089.1
taxid: 100902222
Drosophila melanogaster mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/flymito.fna.gz
vulgarname: flymito
accession: NC_024511.2
taxid: 72272222
Aedes aegypti mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/aedesaegyptimito.fna.gz
vulgarname: aedesaegyptimito
accession: NC_035159.1
taxid: 71592222
Zebrafish mitochondrion:
URL: https://raw.githubusercontent.com/WardDeb/customcontamination/main/fna/zebramito.fna.gz
vulgarname: zebrafishmito
accession: NC_002333.2
taxid: 79552222