README.md

RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

RESCRIPt is a python 3 package to support a variety of operations for managing and curating reference sequence databases, DNA/RNA sequence data, and taxonomic data. See citation information below for a full benchmark and description.

Install via QIIME 2.

RESCRIPt is now installed as part of QIIME 2, and you can install as outlined in the QIIME 2 Documentation, for:

• "Shotgun Distribution" version 2023.9 and later.
• "Amplicon Distrubtion" version 2024.2 and later.

Prior versions of RESCRIPt / QIIME 2.

For details on how to install prior and minimal versions of RESCRIPt for the various versions of QIIME 2, please see the install-prior-versions.md document.

Read help documentation

To view a help menu for using RESCRIPt via the QIIME 2 CLI:

qiime dev refresh-cache
qiime rescript --help

Using RESCRIPt

These tutorials demonstrate some of the basic functionality of RESCRIPt, via the q2CLI (QIIME 2 command-line interface):

• General Overview and working with SILVA data
• Getting sequences and taxonomy with get-ncbi-data
• Building a COI database with BOLD sequences
• Building a COI database with NCBI sequences
• Using RESCRIPt's 'extract-seq-segments' to extract reference sequences without PCR primer pairs
• How to train a GTDB SSU classifier using RESCRIPt
• Constructing an RDP classifier
• How to train a UNITE classifier using RESCRIPt

Examples of visualizations produced by RESCRIPt actions can be found in this Visualization Gallery. Other code examples can be found here.

Getting Help

Problem? Suggestion? Technical errors and user support requests can be filed on the QIIME 2 Forum.

Citation

If you use RESCRIPt in your research, please cite the following:

Michael S Robeson II, Devon R O'Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich. (2021) RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Computational Biology 17 (11): e1009581. doi: 10.1371/journal.pcbi.1009581.

License

RESCRIPt is released under a BSD-3-Clause license. See LICENSE for more details.

However, other resources accessible via RESCRIPt are released under different licenses, as detailed below.

If using the SILVA database (e.g., with get-silva-data): Versions are released under different licenses. Refer to the current SILVA release license information for more details. How to cite SILVA.

If using NCBI Genbank data (e.g., with get-ncbi-data): See the NCBI disclaimer and copyright notice for more details. How to cite NCBI.

If using GTDB data (e.g., with get-gtdb-data): See the GTDB "about" page for more details. How to cite GTDB.

If using UNITE data (e.g., with get-unite-data): See the UNITE citation page for more details. How to cite UNITE.