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Human herpesvirus 2 sequence is absent from the Viral Kraken Database (and all the derivate Databases). It's strange because:
Is there a specific reason why it is missing? Here some simple code for reproducibility:
# get krakendb viral taxa $ wget https://genome-idx.s3.amazonaws.com/kraken/viral_20231009/library_report.tsv $ grep "herpesvirus 2" library_report.tsv | cut -f 2 | sort > krakendb.txt # get RefSeq viral taxas $ wget https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz $ zgrep "^>" viral.1.1.genomic.fna.gz | grep "herpesvirus 2" | sort > viralgenomic.txt # find differences $ diff -y krakendb.txt viralgenomic.txt >NC_001350.1 Saimiriine herpesvirus 2 complete genome >NC_001350.1 Saimiriine herpesvirus 2 complete genome >NC_001650.2 Equid herpesvirus 2 strain 86/67, complete genom >NC_001650.2 Equid herpesvirus 2 strain 86/67, complete genom > >NC_001798.2 Human herpesvirus 2 strain HG52, complete genome >NC_002229.3 Gallid herpesvirus 2, complete genome >NC_002229.3 Gallid herpesvirus 2, complete genome >NC_003521.1 Panine herpesvirus 2 strain Heberling, complete >NC_003521.1 Panine herpesvirus 2 strain Heberling, complete >NC_006560.1 Cercopithecine herpesvirus 2, complete genome >NC_006560.1 Cercopithecine herpesvirus 2, complete genome >NC_007646.1 Ovine herpesvirus 2 strain BJ1035, complete geno >NC_007646.1 Ovine herpesvirus 2 strain BJ1035, complete geno >NC_007653.1 Papiine herpesvirus 2, complete genome >NC_007653.1 Papiine herpesvirus 2, complete genome >NC_008210.1 Ranid herpesvirus 2 strain ATCC VR-568, complete >NC_008210.1 Ranid herpesvirus 2 strain ATCC VR-568, complete >NC_019495.1 Cyprinid herpesvirus 2 strain ST-J1, complete ge >NC_019495.1 Cyprinid herpesvirus 2 strain ST-J1, complete ge >NC_020231.1 Caviid herpesvirus 2 strain 21222, complete geno >NC_020231.1 Caviid herpesvirus 2 strain 21222, complete geno >NC_024382.1 Alcelaphine herpesvirus 2 isolate topi-AlHV-2, c >NC_024382.1 Alcelaphine herpesvirus 2 isolate topi-AlHV-2, c >NC_036579.1 Ictalurid herpesvirus 2 strain 760/94, complete >NC_036579.1 Ictalurid herpesvirus 2 strain 760/94, complete >NC_038265.1 Porcine lymphotropic herpesvirus 2 isolate 568 l >NC_038265.1 Porcine lymphotropic herpesvirus 2 isolate 568 l >NC_038860.1 Pongine herpesvirus 2 (Orangutan herpesvirus) gB >NC_038860.1 Pongine herpesvirus 2 (Orangutan herpesvirus) gB >NC_043042.1 Acipenserid herpesvirus 2 strain SRWSHV, partial >NC_043042.1 Acipenserid herpesvirus 2 strain SRWSHV, partial >NC_043044.1 Salmonid herpesvirus 2 isolate NeVTA ORF68-like >NC_043044.1 Salmonid herpesvirus 2 isolate NeVTA ORF68-like >NC_043059.1 Caprine herpesvirus 2 glycoprotein B (gB) and DN >NC_043059.1 Caprine herpesvirus 2 glycoprotein B (gB) and DN >NC_043062.1 Phocid herpesvirus 2 DNA-dependent DNA polymeras >NC_043062.1 Phocid herpesvirus 2 DNA-dependent DNA polymeras >NC_043063.1 Iguanid herpesvirus 2 DNA-dependent DNA polymera >NC_043063.1 Iguanid herpesvirus 2 DNA-dependent DNA polymera >NC_075563.1 Cervid alphaherpesvirus 2 strain Norway, complet >NC_075563.1 Cervid alphaherpesvirus 2 strain Norway, complet >NC_075802.1 Salmonid herpesvirus 2 isolate NeVTA DNA polymer >NC_075802.1 Salmonid herpesvirus 2 isolate NeVTA DNA polymer >NC_076512.1 Bovine alphaherpesvirus 2 strain C1Z FZR, comple >NC_076512.1 Bovine alphaherpesvirus 2 strain C1Z FZR, comple >NC_076513.1 Macropodid alphaherpesvirus 2 strain V3077/08, c >NC_076513.1 Macropodid alphaherpesvirus 2 strain V3077/08, c >NC_076966.1 Cacatuid alphaherpesvirus 2 isolate CaHV2/Melbou >NC_076966.1 Cacatuid alphaherpesvirus 2 isolate CaHV2/Melbou
The text was updated successfully, but these errors were encountered:
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Human herpesvirus 2 sequence is absent from the Viral Kraken Database (and all the derivate Databases).
It's strange because:
Is there a specific reason why it is missing?
Here some simple code for reproducibility:
The text was updated successfully, but these errors were encountered: