Galaxy |

NCBI-GTDB map (version 0.1.9+galaxy0)

File with the names:

You can either have a file the NCBI names or the GTDB names

Use either a cached ncbi database or upload from history:

Metadata version:

Choose metadata version

Select the type of mapping:

Choose if you want to map NCBI agaisnt GTDB or the other way around

Completeness filter:

Only include GTDB genomes who have bigger or equal CheckM completeness

Contamination filter:

Only include GTDB genomes who have a smaller CheckM contamination

Homogeneity of LCA:

Change the homogeneity of LCA in order to be used

Max. number of tips:

Select the number of tips used for LCA determination

Select the column with the names:

Header row in the input:

Check if the input file has a header to so the program will skip it

Add prefix to the names?:

Select yes if you want to add a prefix to the names

No prefix:

Check here if the names doesn't have a prefix like 's__xyz'. NOTE: Only names without prefix will be used then when a name still have it it will be mapped to unclassified!

Where to download the metadata

The metadata can be download from GTDB. If you want to use this tool to convert gtdb naming from a GTDB tool such as gtdbtk classify_wf use the corresponding GTDB release of the metadata. After download it dont forget to uncompressed it!

What does this tool

This tool was desinged to map the GTDB taxonomy to the NCBI taxonomy since both are using different ID systems. This means this tool map either GTDB names to the NCBI names or the other way around. If the names contain prefixes like s__ the mapped name also will contain there corresponded prefix. If you use the names without prefix then the mapped names also don't contain the prefixes.

Prefixes

The prefixes stand for the taxonomic rank for example s__Bacteroides thetaiotaomicron. If you use them directly with in the file where you list the names which should be queried then you dont need the prefix option but if you use names without them you can either manully include them with the prefix option (read the help section there too) or you can use the tool without them but then you have to check the no-prefix option! This means when you use the no-prefix option s__Bacteroides thetaiotaomicron will not be used in this tool but Bacteroides thetaiotaomicron will work fine!