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SSUextract

SSUextract searches assembled contigs for 16S rRNA genes and 18S rRNA genes. It extracts each complete Infernal hit interval and assigns taxonomy with the reference database for that marker.

Run the bundled example · Parameters · Output files

Pipeline

SSUextract pipeline from Infernal detection and marker-specific BLAST through default BLAST taxonomy or optional tree-neighbor classification

Run the bundled example

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

pixi run setup lists the database profiles. A new checkout defaults to curated; later runs use the saved selection. Before Nextflow starts, an interactive run offers to install a newer database release when one is available. The example writes extracted sequences, per-hit annotations, category counts, and Nextflow reports under results/smoke/.

Steps

  1. Infernal searches each assembly with 16S rRNA gene and 18S rRNA gene covariance models.
  2. Overlapping RF00177 and RF01960 hits on the same strand compete by Infernal E-value, then bit score.
  3. SSUextract extracts each retained interval on the reported strand.
  4. Each sequence is searched against the 16S rRNA gene or 18S rRNA gene index selected by its model.
  5. By default, equal-best BLAST subjects determine taxonomy. Tree mode instead aligns the query with 100 references and assigns taxonomy from its nearest named tree neighbors.
  6. The workflow writes extracted FASTA files, one row per hit, reference evidence, category counts, and execution reports.

Pipeline details · Run assembled genomes or metagenomes