Skip to content

Commit

Permalink
Update doc, fix typo
Browse files Browse the repository at this point in the history
  • Loading branch information
pchaumeil committed Apr 4, 2022
1 parent 9a4c1b5 commit 7fe04c3
Showing 1 changed file with 8 additions and 7 deletions.
15 changes: 8 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -17,15 +17,16 @@ Notifications about GTDB-Tk releases will be available through the GTDB Twitter
Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions related to the [GTDB](https://gtdb.ecogenomic.org/) should be sent to the [GTDB team](https://gtdb.ecogenomic.org/about).

## New Features
GTDB-Tk v2.0.1+ includes the following new features:
- Classification is done by default using a divide-and-conquer strategy to systematically reduce the size of the reference tree and associated memory requirements.
When runnning with R07-RS207, GTDB-Tk requieres **320GB** or RAM when running pplacer with the full bacterial tree. The divide and conquer approach reduve this requirement to around **20GB** of RAM.
**This is now the default option strategy in GTDB-Tk.**
- To use the full reference tree in the classification step, use the `-f,--full-tree` option.
- Use of a refined set of 53 archaeal-specific marker genes based on a recent published analysis of archaeal markers.
GTDB-Tk v2.0.1 includes the following new features:
- Classification is done by default using a **divide-and-conquer** strategy to systematically reduce the size of the reference tree and associated memory requirements.
When running with R07-RS207, GTDB-Tk requires **320GB** of RAM for the pplacer step with the full bacterial tree.
The divide-and-conquer approach reduces this requirement to around **20GB** of RAM.
**This is now the default approach in GTDB-Tk.**
To use the full bacterial reference tree in the classification step, use the `-f,--full-tree` flag.
- Archaeal classification now uses a refined set of 53 archaeal-specific marker genes based on a recent published analysis of archaeal markers (similar to GTDB R07-RS207).
- To reduce the size of the output directory,
- all intermediate_results folders ( in _identify,align,classify,infer_) are **now removed** after the end of the `classify_wf` and `de_novo_wf` pipelines. To keep intermediates files use the flag `--keep-intermediates`.
- all msa output from the align step are now automatically archived.
- all msa output from the align step are now automatically archived (_.gz)_.


## Documentation
Expand Down

0 comments on commit 7fe04c3

Please sign in to comment.