sbx_vsearch

A Sunbeam extension for using Vsearch with the --usearch-global option to do alignment of reads to any fasta file.

Installation

To install, activate your conda environment (using the name of your environment) and use sunbeam extend:

conda activate <i>sunbeamX.X.X</i>
sunbeam extend https://github.com/sunbeam-labs/sbx_vsearch.git

Usage

To run vsearch:

sunbeam init --data_fp /path/to/reads/ /path/to/project/
sunbeam config modify -i -f /path/to/project/sunbeam_config.yml -s 'sbx_vsearch: {{db: {/path/to/db}}}'
sunbeam run --profile /path/to/project/ all_vsearch

N.B. For sunbeam versions <4 the last command will be something like sunbeam run --configfile /path/to/project/sunbeam_config.yml all_classify.

Configuration

• db_fp: Is the filepath to a directory containing reference fasta files
• threads: Is the number of threads to use while running vsearch
• min_id: Is the minimum identity for query-target match
• weak_id: Is the set lower than min-id and you will get some weaker matches too
• userfields: Are the fields for results file, see vsearch - documentation for details
• iddef: Is the way "identity" is calculated, see vsearch docs for details (it's equal to (matching columns) / (alignment length) excluding terminal gaps)
• fasta_width: Is the width of alignment lines in fasta output, set to 0 to eliminate wrapping
• maxaccepts: Is the maximum number of hits to accept before stopping the search Default is 1

Legacy Installation

For sunbeam versions <3 or if sunbeam extend isn't working, you can use git directly to install an extension:

git clone https://github.com/sunbeam-labs/sbx_vsearch.git extensions/sbx_vsearch

and then include it in the config for any given project with:

cat extensions/sbx_vsearch/config.yml >> /path/to/project/sunbeam_config.yml