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.
RESCRIPt will be installable as conda package in the near future. In the meantime, we provide two routes for source installation: a minimal RESCRIPt environment, or within an existing QIIME 2 environment:
First create a conda environment and install relevant dependencies:
conda create -y -n rescript
conda activate rescript
conda install \
-c conda-forge -c bioconda -c qiime2 -c defaults \
qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier "pandas>=0.25.3" xmltodict
Install source:
pip install git+https://github.com/bokulich-lab/RESCRIPt.git
First activate your QIIME 2 environment (ver 2021.4 or later) and install relevant dependencies:
conda activate qiime2-2021.4
conda install -c conda-forge -c bioconda -c qiime2 -c defaults xmltodict
Install source:
pip install git+https://github.com/bokulich-lab/RESCRIPt.git
To view a help menu for using rescript via the QIIME 2 CLI:
qiime dev refresh-cache
qiime --help
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
Examples of visualizations produced by RESCRIPt actions can be found in this Visualization Gallery.
Problem? Suggestion? Technical errors and user support requests can be filed on the QIIME 2 Forum.
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.
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.
The SILVA database versions are released under different licenses. Refer to the current SILVA release license information for more details.
If using NCBI Genbank data (e.g., with get-ncbi-data): See the NCBI disclaimer and copyright notice