sbx_mapping

A Sunbeam extension for mapping reads against a set of reference genomes.

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_mapping.git

Usage

To generate coverage reports, create a project, specify your references, and use the all_mapping target:

sunbeam init --data_fp /path/to/reads/ /path/to/project/
sunbeam config modify -i -f /path/to/project/sunbeam_config.yml -s 'sbx_mapping: {{genomes_fp: {/path/to/uncompressed/fasta/reference/genomes/}}}'
sunbeam run --profile /path/to/project/ all_mapping

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

Configuration

• genomes_fp: Is the filepath to your reference genomes (in fasta format) all references must have .fasta OR .fa OR .fna extension!!
• samtools_opts: Are the options passed to samtools view
• alnLen: Is the minimum alignment length
• percIdentity: Is the minimum percent identity
• window_size: Is the size of the sliding window for coverage calculations
• sampling: Is the sampling rate for coverage calculations

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_mapping.git extensions/sbx_mapping

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

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