Metagenomic tools like Kraken2, Centrifuge and KMCP support NCBI taxonomy in format of NCBI taxdump files.
While for virus, ICTV (International Committee on Taxonomy of Viruses) has its own taxonomy data.
A TaxonKit command, taxonkit create-taxdump is created
to create NCBI-style taxdump files for any taxonomy dataset,
including GTDB and ICTV.
Related projects:
- gtdb-taxdump: GTDB taxonomy taxdump files with trackable TaxIds
- taxid-changelog: NCBI taxonomic identifier (taxid) changelog
- taxonkit: A Practical and Efficient NCBI Taxonomy Toolkit
The release page contains taxdump files.
Virus Metadata Resource (VMR) provides taxonomy data of each release. Most viruses have the seven-ranks (Kingdom, Phylum, Class, Order, Family, Genus, Species), and each has a name.
Optionally, we assign the virus name a TaxId with the rank of "subspecies" below the species rank. Therefore, we can also track the changes of these assemblies via the TaxId later.
We just hash the taxon name (in lower case) of each taxon node to uint64
using xxhash and convert it to int32.
Taxa from different parents may have the same name. We assign different TaxIds to them. E.g., many viruses from different species have the same names.
Species Virus name(s)
Jerseyvirus SETP3 Salmonella phage SETP7
Jerseyvirus SETP7 Salmonella phage SETP7
$ grep 'Salmonella phage SETP7' ictv-taxdump-with-subspecies/taxid.map
Salmonella phage SETP7 2451596205,2451596206
$ grep 'Salmonella phage 3-29' ictv-taxdump-with-subspecies/taxid.map \
| csvtk unfold -Ht -f 2 -s , \
| taxonkit reformat -f 'genus: {g}, species: {s}, subspecies: {S}' \
--data-dir ictv-taxdump-with-subspecies/ -I 2
Salmonella phage 3-29 3010875164 genus: Epseptimavirus, species: Epseptimavirus ev329, subspecies: Salmonella phage 3-29
Salmonella phage 3-29 3010875165 genus: Epseptimavirus, species: Salmonella virus 329, subspecies: Salmonella phage 3-29
The taxonomy data is released as a .xlsx file at https://talk.ictvonline.org/taxonomy/vmr/.
TaxonKit v0.12.0 or a later version is needed.
v0.14.0 or a later version is preferred.
Since v0.14.0, taxonkit create-taxdump stores
TaxIds in int32 following BLAST and DIAMOND, rather than uint32 in previous versions.
# download here: https://talk.ictvonline.org/taxonomy/vmr/
file="VMR_19-250422_MSL37.xlsx"
# conver xlsx to tsv
csvtk xlsx2csv "$file" \
| csvtk csv2tab \
> ictv.tsv
# remove M-BM- characters.
# https://askubuntu.com/questions/357248/how-to-remove-special-m-bm-character-with-sed
sed -i 's/\xc2\xa0/ /g' ictv.tsv
# remove leading and tailing blanks. e.g., "Escherichia phage PhaxI\t"
# remove a newline character and a space introduced by accident
csvtk replace -t -F -f "*" -p "^\s+|\s+$" ictv.tsv \
| csvtk replace -t -F -f "*" -p "\n " -r "" \
> ictv.clean.tsv
# choose columns, rename, and remove duplicates
csvtk cut -t -f "Realm,Subrealm,Kingdom,Subkingdom,Phylum,Subphylum,Class,Subclass,Order,Suborder,Family,Subfamily,Genus,Subgenus,Species,Virus name(s)" ictv.clean.tsv \
| csvtk rename -t -f 1-16 -n "realm,subrealm,kingdom,subkingdom,phylum,subphylum,class,subclass,order,suborder,family,subfamily,genus,subgenus,species,subspecies" \
| csvtk uniq -t -f 1-16 \
> ictv.taxonomy.tsv
# ------------------- create-taxdump -----------------------
# Option A: the lowest rank is species
taxonkit create-taxdump -A 16 --field-accession-re "^(.+)$" \
ictv.taxonomy.tsv --out-dir ictv-taxdump/
# Option B: treat "Virus name(s)" as subspecies
taxonkit create-taxdump -A 16 --field-accession-re "^(.+)$" \
ictv.taxonomy.tsv --out-dir ictv-taxdump-with-subspecies/ \
--field-accession-as-subspecies
# ictv-taxdump/ is a subset of ictv-taxdump-with-subspecies/
# set the environmental variable for taxonkit,
# so we don't need specifiy "--data-dir ictv-taxdump" for each taxonkit command.
export TAXONKIT_DB=ictv-taxdump
Set the environmental variable for taxonkit,
so we don't need specifiy --data-dir ictv-taxdump for each taxonkit command.
export TAXONKIT_DB=ictv-taxdump-with-subspecies
Check more TaxonKit commands and usages
-
Count of all ranks (version: Virus Metadata Repository number 19, April 25 2022; MSL37)
$ taxonkit list --ids 1 \ | taxonkit lineage -L -r \ | csvtk freq -H -t -f 2 -n \ | csvtk pretty -H -t no rank 1 subphylum 2 realm 6 suborder 8 kingdom 10 phylum 17 class 39 order 65 subgenus 84 subfamily 168 family 233 genus 2606 species 10434 subspecies 10539
-
The TaxId
$ grep 'severe acute respiratory syndrome coronavirus 2' ictv-taxdump-with-subspecies/taxid.map severe acute respiratory syndrome coronavirus 2 216305222 -
Complete lineage
$ echo 216305222 | taxonkit lineage 216305222 Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severe acute respiratory syndrome-related coronavirus;severe acute respiratory syndrome coronavirus 2 # another format $ echo 216305222 \ | taxonkit lineage -t \ | csvtk cut -Ht -f 3 \ | csvtk unfold -Ht -f 1 -s ";" \ | taxonkit lineage -r -n -L \ | csvtk cut -Ht -f 1,3,2 \ | csvtk pretty -Ht 492247681 realm Riboviria 104708768 kingdom Orthornavirae 1506901452 phylum Pisuviricota 1091693597 class Pisoniviricetes 37745009 order Nidovirales 242661632 suborder Cornidovirineae 738421640 family Coronaviridae 1428506634 subfamily Orthocoronavirinae 906833049 genus Betacoronavirus 605136173 subgenus Sarbecovirus 1015862491 species Severe acute respiratory syndrome-related coronavirus 216305222 subspecies severe acute respiratory syndrome coronavirus 2 # in NCBI taxonomy $ echo 2697049 \ | taxonkit lineage -t --data-dir ~/.taxonkit \ | csvtk cut -Ht -f 3 \ | csvtk unfold -Ht -f 1 -s ";" \ | taxonkit lineage -r -n -L --data-dir ~/.taxonkit \ | csvtk cut -Ht -f 1,3,2 \ | csvtk pretty -Ht 10239 superkingdom Viruses 2559587 clade Riboviria 2732396 kingdom Orthornavirae 2732408 phylum Pisuviricota 2732506 class Pisoniviricetes 76804 order Nidovirales 2499399 suborder Cornidovirineae 11118 family Coronaviridae 2501931 subfamily Orthocoronavirinae 694002 genus Betacoronavirus 2509511 subgenus Sarbecovirus 694009 species Severe acute respiratory syndrome-related coronavirus 2697049 no rank Severe acute respiratory syndrome coronavirus 2
For examples species Epseptimavirus ev329 and Salmonella virus 329 both have a "Virus name" Salmonella phage 3-29.
$ cat ictv.taxonomy.tsv \
| csvtk grep -t -f subspecies -p 'Salmonella phage 3-29' \
| csvtk cut -t -f genus,species,subspecies \
| csvtk pretty -t
genus species subspecies
-------------- -------------------- ---------------------
Epseptimavirus Epseptimavirus ev329 Salmonella phage 3-29
Epseptimavirus Salmonella virus 329 Salmonella phage 3-29
They are assigned with different TaxIds and can be queried in taxid.map:
$ grep 'Salmonella phage 3-29' ictv-taxdump-with-subspecies/taxid.map
Salmonella phage 3-29 863391516,863391517
$ grep 'Salmonella phage 3-29' ictv-taxdump-with-subspecies/taxid.map \
| csvtk unfold -Ht -f 2 -s , \
| taxonkit lineage --data-dir ictv-taxdump-with-subspecies/ -i 2
Salmonella phage 3-29 863391516 Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Demerecviridae;Markadamsvirinae;Epseptimavirus;Epseptimavirus ev329;Salmonella phage 3-29
Salmonella phage 3-29 863391517 Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Demerecviridae;Markadamsvirinae;Epseptimavirus;Salmonella virus 329;Salmonella phage 3-29
Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit, Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006
We welcome pull requests, bug fixes and issue reports.