A Sunbeam extension to perform co-assembly of reads from arbitrary groups of samples from a given project using Megahit.
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_coassembly.git
To generate coassembled samples, create a project, define your groupings, and use the all_coassemble target:
sunbeam init --data_fp /path/to/reads/ /path/to/project/
printf "A: ['A_d1', 'A_d2', 'A_d3']\nB: ['B_d1', 'B_d3']" > mapping.yml
sunbeam config modify -i -f /path/to/project/sunbeam_config.yml -s 'sbx_coassembly: {{group_file: {/path/to/mapping.yml}}}'
sunbeam run --profile /path/to/project/ all_coassemble
N.B. For sunbeam versions <4 the last command will be something like sunbeam run --configfile /path/to/project/sunbeam_config.yml all_coassemble.
If you'd like to coassemble all of your samples, no further input is needed!
If no grouping file is specified this extension by default co-assembles all samples. If you'd like to group specific samples, you need to provide a mapping file, then point to that mapping file in your config file. For example, if you have three samples from individual A (A_d1, A_d2, A_d3) and two from individual B (B_d1, B_d3), and you'd like to make one coassembly for each individual, you first need a mapping file like this (I'll call it mapping.yml):
A: ['A_d1', 'A_d2', 'A_d3']
B: ['B_d1', 'B_d3']
Here, the bracketed items in the list (i.e. 'A_d1' or 'B_d3' are your full sample names and must match the sample names Sunbeam knows. (Look in your samples.csv file if you're not sure of the names). The keys at the beginning of the lines are the group names--you can use any valid Python variable name here. After making this mapping file, make sure to edit your config file to point to this mapping file:
...
sbx_coassembly:
threads: 4
group_file: '/path/to/mapping.yml'
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_coassembly.git extensions/sbx_coassembly
and then include it in the config for any given project with:
cat extensions/sbx_coassembly/config.yml >> /path/to/project/sunbeam_config.yml