satannot is a Python tool for BLAST-based annotation and sequence extraction. It provides functionalities for running BLAST searches, filtering results, and extracting sequences based on user-defined criteria.
Features
- Annotation: Annotate sequences using BLAST with customizable filtering options.
- Extraction: Extract sequences based on annotations in GFF format.
Ensure the following are installed on your system:
- Python: Version 3.8 or higher.
- NCBI BLAST+: Required for BLAST-based operations.
If you don't have NCBI-BLAST installed, best is done so with mamba/conda and to install satannot in a environment:
mamba create -c bioconda -c conda-forge -n satannot python=3.12 blast
mamba activate satannot
Then you can install satannot directly from GitHub:
pip install git+https://github.com/mvolar/satannot.git
Run BLAST-based annotation and output results in GFF format followed by extractiong of FASTA sequences:
satannot annotate query.fasta genome.fasta --gff_out annotations.gff
Optional parameters:
--perc_id_filter: Minimum percentage identity (default: 70.0).
--qcovhsp_filter: Minimum query coverage per HSP (default: 70.0).
satannot extract genome.fasta annotations.gff output_directory
This project is licensed under the MIT License (LICENSE).
Contributions are welcome! Feel free to submit issues or pull requests to enhance the tool.
If you use SatAnnot in you work please cite:
Marin Volarić, Nevenka Meštrović, Evelin Despot-Slade,
SatXplor—a comprehensive pipeline for satellite DNA analyses in complex genome assemblies, Briefings in Bioinformatics, Volume 26, Issue 1, January 2025, bbae660, https://doi.org/10.1093/bib/bbae660