A Sunbeam extension for estimating bacterial growth rates via peak-to-trough ratios (PTRs) using DEMIC. In preparation to use demic, reads are first assembled using Megahit, then binned by inferred genome using MaxBin2, after which reads are mapped back onto contigs using Bowtie2 and Samtools.
Note: The original paper for demic can be found here and the associated software here. A lot of work has gone into demic since publication to make it more reliable, installable, and easy to use. The main functionality of demic is now housed in a python library for generating special coverage files (pycov3) and an R package for estimating PTRs from these coverage files (DEMIC).
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_demic.git
To generate PTRs, create a project and use the all_demic target:
sunbeam init --data_fp /path/to/reads/ /path/to/project/
sunbeam run --profile /path/to/project/ all_demic
- coassembly_threads: Is the number of threads to use in assembly steps
- group_file: Is the path to the coassembly group file, leave blank to treat all samples as one group
- demic_threads: Is the number of threads to use in the binning, mapping, and estimation steps
- single_genome: Should be true if your samples only contain a single genome, false otherwise
- extras: Are parameters to be passed to PyCov3
Note: See sbx_coassembly README for more information on how to group samples with the group_file. See PyCov3 for more information on what parameters can be passed for coverage generation.
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_demic.git extensions/sbx_demic
and then include it in the config for any given project with:
cat extensions/sbx_demic/config.yml >> /path/to/project/sunbeam_config.yml