benkaehler/rescript

REference Sequence annotation and CuRatIon Pipeline

RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

Note: This is a beta release. Usage, and other details are forthcoming. See citation information below.

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.

Install from source

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:

Option 1: Minimal RESCRIPt 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

Option 2: Install within QIIME 2 environment

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

Read help documentation

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

qiime dev refresh-cache
qiime --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

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 pre-print:

Michael S Robeson II, Devon R O'Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich. RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. bioRxiv 2020.10.05.326504; doi: https://doi.org/10.1101/2020.10.05.326504

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.

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