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README: Document the type material filter option
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Signed-off-by: Kai Blin <[email protected]>
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kblin committed Jan 23, 2019
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Expand Up @@ -177,6 +177,16 @@ There is a "dry-run" option to show which accessions would be downloaded, given
ncbi-genome-download --dry-run bacteria
```

If you want to filter for the "relation to type material" column of the
assembly summary file, you can use the `--type-material` option. Possible
values are "any", "all", "type", "reference", "synonym", "proxytype", and/or
"neotype". "any" will include assemblies with no relation to type material
value defined, "all" will download only assemblies with a defined value.
Multiple values can be given, separated by comma:
```
ncbi-genome-download --type-material type,reference
```

By default, ncbi-genome-download caches the assembly summary files for the respective taxonomic
groups for one day. You can skip using the cache file by using the `--no-cache` option.
The output of `--help` also shows the cache directory, should you want to remove any of the cached
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