sbx_assembly

A Sunbeam extension for assembly of contigs using Megahit, gene annotation using Prodigal, and annotation using Blast and Diamond. It can also map reads to contigs and calculat per-base coverage using Minimap2 and samtools.

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_assembly.git

Usage

To generate contigs, annotations and coverage, create a project and use the all_assembly, all_annotation, and all_coverage targets:

sunbeam init --data_fp /path/to/reads/ /path/to/project/
sunbeam run --profile /path/to/project/ --target_list all_assembly all_annotate

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

Configuration

Assembly

• min_length: Is the minimum contig length to accept in the final filtering Annotation
• threads: Is the number of threads to use running blast/diamond
• circular_kmin: Is the minimum length of overlap to check for circular contigs with
• circular_kmax: Is the maximum length of overlap to check for circular contigs with
• circular_min_len: Is the minimum sequence length to consider checking for circularity Coverage
• threads: Is the number of threads to use while running minimap2 and samtools sort

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_assembly.git extensions/sbx_assembly

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

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