cblaster-genome

Summary of cblaster-genome results from project: [mq_saccharopolyspora]

Description

Build a diamond database of all genomes in the project for clustered hits from a BLAST search using cblaster.

How to run query from local database

• Download all files from the CBlaster result:

CBlaster database

• Install CBlaster conda environment using this yaml configuration (create a file called env.yaml and copy paste the following items to the file). See the conda guide here:

name: cblaster
channels:
  - conda-forge
  - default
  - bioconda
dependencies:
  - diamond==2.0.15
  - pip
  - pip:
    - cblaster==1.3.12

• After having the environment installed, cd to the directory containing all the files, activate the environment, and run queries by:

# activate environment
conda activate cblaster
cblaster search -m local -db cblaster_genome_db.dmnd -qf <query.faa>

• See CBlaster guide for running local queries here

References

• Gilchrist, C., Booth, T. J., van Wersch, B., van Grieken, L., Medema, M. H., & Chooi, Y. (2021). cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters (Version 1.3.9) [Computer software]. https://doi.org/10.1101/2020.11.08.370601

• Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).