User Guide ========== Update: What's New in run_dbCAN ================================ The new version of **run_dbCAN** introduces multiple new features and significant performance improvements, making the pipeline more user-friendly and efficient. We highly recommend users to upgrade to this version. If you have any questions or suggestions, please feel free to contact us: * Dr. Yanbin Yin, Professor (yyin@unl.edu) * Xinpeng Zhang, PhD Student (xzhang55@huskers.unl.edu) * Dr. Haidong Yi, Software Engineer (hyi@stjude.org) All conda environments dependencies can be found at the following link: `run_dbCAN Conda Environments `_ Key Features and Improvements ----------------------------- 1. **Simplified Database Downloading** - Added a new `database` command for downloading database files, making the process simpler than before. - Supports downloading from both HTTP and AWS S3 sources (use `--aws_s3` flag for faster and more stable downloads). - Use `--cgc/--no-cgc` option to control whether to download CGC-related databases. 2. **Enhanced Input Processing** - Replaced `prodigal` with `pyrodigal `_ for input processing. 3. **Improved HMMER Performance** - Replaced `HMMER` with `pyHMMER `_, which is faster and more efficient. - Redesigned memory usage to support both low-memory and high-efficiency modes (https://pyhmmer.readthedocs.io/en/stable/examples/performance_tips.html). 4. **Modular Code Structure** - Reorganized the logic and structure of `run_dbCAN` by splitting functions into modules and following Object Oriented Programming. - Rewrote non-Python code in Python for improved readability. - Centralized parameter management using configuration files. - Leveraged the power of `pandas` for efficient data processing. - Added extensive logging and time reporting to make the pipeline more user-friendly. 5. **Enhanced dbCAN-sub and overview Features** - Added coverage justifications and location information for dbCAN-sub. - Included CAZyme justification in the final results with an extra column called "Best Results." - Now follow the rule: `CAZy-sub > dbCAN-sub > dbCAN-fam` for the final results. 6. **Redesigned CGCFinder** - Now supports JGI, NCBI, and Prodigal gff formats. - Directly searches eukaryotic genomes, including fungi (**beta function**). - Added a new function to visualize the CGCs on the genome (**beta function**). 7. **Faster Substrate Prediction** - Replaced `blastp` with `DIAMOND` for substrate prediction, significantly improving speed and efficiency. 8. **Updated Metagenomic Protocols** - Improved steps for metagenomic data processing (https://www.biorxiv.org/content/10.1101/2024.01.10.575125v1). 9. **SignalP 6.0 and DeepTMHMM (optional topology)** - **SignalP 6.0**: signal peptide prediction in the `CAZyme_annotation` command via `--run_signalp`. Results are merged into `overview.tsv` in a **SignalP** column. Organism class: `--signalp_org` (`other` / `euk`). - **DeepTMHMM**: transmembrane topology via `--run_deeptmhmm` and `--deeptmhmm_dir` (directory containing the user-installed `predict.py`). Results are merged into **DeepTMHMM** in `overview.tsv`. - Neither tool is bundled with `dbcan`. Install and test them locally, then enable the flags. See :doc:`user_guide/signalp6_deeptmhmm` and the `SignalP 6.0 installation instructions `_. 10. **Global Logging System** - Implemented comprehensive logging system available for all commands. - Use `--log-level` to set logging level (DEBUG/INFO/WARNING/ERROR/CRITICAL, default: WARNING). - Use `--log-file` to write logs to a file in addition to console output. - Use `--verbose` or `-v` flag for detailed debug logging (equivalent to --log-level DEBUG). .. hint:: If you want to run the pipeline from raw metagenomic reads, please refer to the following part: **metagenomics_pipeline** Otherwise, refer to the instructions below. Please note that some precomputed results may have different names compared to the previous version. .. note:: For detailed instructions, refer to the respective sections in the documentation. .. toctree:: :maxdepth: 1 :caption: Getting start getting_started/installation getting_started/database_description getting_started/quick_start .. toctree:: :maxdepth: 1 :caption: User guide user_guide/prepare_the_database user_guide/CAZyme_annotation user_guide/signalp6_deeptmhmm user_guide/CGC_information_generation user_guide/CGC_annotation user_guide/predict_CGC_substrate user_guide/CGC_plots .. toctree:: :maxdepth: 1 :caption: Comparison comparison/CAZyme_annotation_compare .. toctree:: :maxdepth: 1 :caption: API api/index .. toctree:: :maxdepth: 1 :caption: Metagenomics pipeline metagenomics_pipeline/run_from_raw_reads metagenomics_pipeline/run_from_raw_reads_am metagenomics_pipeline/run_from_raw_reads_pr metagenomics_pipeline/run_from_raw_reads_wk metagenomics_pipeline/run_from_raw_reads_em metagenomics_pipeline/supplement/run_from_raw_reads_sp_co_assem metagenomics_pipeline/supplement/run_from_raw_reads_sp_subsample metagenomics_pipeline/supplement/run_from_raw_reads_sp_assem_free .. toctree:: :maxdepth: 1 :caption: Nextflow Pipeline nextflow/index .. toctree:: :maxdepth: 1 :caption: Change logs change-logs/index .. toctree:: :maxdepth: 1 :caption: References references/index .. toctree:: :maxdepth: 1 :caption: Contributors contributors/index