sbx_cenote_taker

Introduction

sbx_cenote_taker is a sunbeam extension for identifying viruses in samples with Cenote-Taker3. This pipeline uses MEGAHIT for assembly of contigs and then processes assemblies with Cenote-Taker3.

N.B. This extension requires also having sbx_assembly installed.

Installation

sunbeam extend https://github.com/sunbeam-labs/sbx_assembly.git
sunbeam extend https://github.com/sunbeam-labs/sbx_cenote_taker.git

Cenote-Taker database

sbx_cenote_taker expects the Cenote-Taker3 reference database to be available locally. Download the database following the official instructions, for example:

conda activate cenote-taker
get_ct3_dbs -o /path/to/ct3_db --hmm T --hallmark_tax T --refseq_tax T --mmseqs_cdd T --domain_list T --hhCDD T --hhPFAM T --hhPDB T

Update the cenote_taker_db entry in your Sunbeam configuration to point at the resulting directory.

Running

Run with sunbeam on the target all_cenote_taker:

sunbeam run --profile /path/to/project/ all_cenote_taker

Options for config.yml

• blast_db: path to blast db (default: "") (NOTE: this should be the database file not just the directory it's in)
• blastx_threads: number of threads for running blastx (default: 4)
• bowtie2_build_threads: number of threads for running bowtie2-build (default: 4)
• cenote_taker_db: path to cenote-taker3 db (default: "") (NOTE: this should be a directory)
• include_phages: Whether to include phages in the output (default: False)