Build a Sourmash Database for Fast Search

Build a database of sourmash signatures from a genomic library.

Usage

1. Set up nextflow as described here.

2. If you didn't run this pipeline in a while, possibly update nextflow itself.

   nextflow self-update

3. Then run the pipeline.

   1. Sequence Bloom Tree (SBT) indexed databases

      nextflow run main.nf --input 'genomes/*.fna'

      We suggest that you make use of one of the provided profiles that enhance reproducibility, i.e., -profile docker|singularity|conda.

      In this form, the pipeline will generate an SBT index, by default, this results in a .sbt.zip file.

   2. Reverse indexed (LCA) databases

      Alternatively, you can provide a taxonomy table similar to the one shown here and invoke the nextflow pipeline with the taxonomy information.

      nextflow run main.nf --input 'genomes/*.fna' --taxonomy 'podar-lineage.csv'

      This will result in an index .lca.json.gz file.

Copyright

• Copyright © 2022 Unseen Bio ApS.
• Free software distributed under the GNU Affero General Public License version 3 or later (AGPL-3.0-or-later).