Databasesο
Markersο
Autometa comes packaged with the necessary markers files. Links to these markers files and their associated cutoff values are below:
NCBIο
If you are running Autometa for the first time you will need to download the NCBI databases. You may do this manually or using a few Autometa helper scripts. If you would like to use Autometaβs scripts for this, you will first need to download Autometa (See Installation).
# First configure where you want to download the NCBI databases
autometa-config \\
--section databases --option ncbi \\
--value <path/to/your/ncbi/database/directory>
# Now download and format the NCBI databases
autometa-update-databases --update-ncbi
Note
You can check the default config paths using autometa-config --print
.
See autometa-update-databases -h
and autometa-config -h
for full list of options.
The previous command will download the following NCBI databases:
- Non-redundant nr database
- prot.accession2taxid.gz
- nodes.dmp, names.dmp and merged.dmp - Found within
After these files are downloaded, the taxdump.tar.gz
tarballβs files are extracted and the non-redundant protein database (nr.gz
)
is formatted as a diamond database (i.e. nr.dmnd
). This will significantly speed-up the diamond blastp
searches.