SSUextract

SSUextract is a Nextflow pipeline that detects 16S rRNA genes and 18S rRNA genes in assembled contigs, extracts complete hit intervals, and assigns taxonomy with marker-specific reference databases.

Quick start

git clone https://github.com/NeLLi-team/ssuextract.git
cd ssuextract
pixi install --frozen
pixi run setup
pixi run example

Add --tree_classification to classify each extracted gene from a local tree of the query and 100 reference sequences:

pixi run ssuextract -q data/my_dataset --outdir results/my_dataset --tree_classification

Tree mode is optional. The default run assigns taxonomy from the highest-scoring BLAST subjects.

-q is the short form of --query in the Pixi wrapper. Both accept one .fna, .fa, or .fasta file or a directory of those files. A single file named sample.fna writes to results/sample unless --outdir is set.

pixi run setup lists the curated and img profiles with their database versions and download sizes. Select a profile by number or name. That selection becomes the default for later pipeline runs. Interactive runs check Zenodo and offer to install a newer release before Nextflow starts. During a download, one terminal line shows written bytes, transfer rate, and estimated time remaining. Rerun the same setup command after an interrupted transfer; it continues from the retained partial archive and verifies the completed archive before extraction.

Documentation: tutorial, parameters, output files, and database profiles.

Run pixi run ssuextract --help to see the command-line summary.

SSUextract is licensed for non-commercial use only.