A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings maybe specific for our compute resources
atavide is a full-fledged metagenome processing pipeline. This is a simpler version that uses either slurm scripts or PBS scripts to accomplish the same things. In this initial release, we avoided snakemake to work through the steps one at a time, although that will likely come soon.
See the verions:
- slurm - designed to work on Flinders deepthought infrastructure
- pbs - designed to work on the NCI infrastructrue for now
Currently the pipeline depends on these software
- fastp
- samtools
- minimap2
- megahit
- mmseqs
- vamb
You can install all of these with:
mamba env create -f ~/atavide_lite/atavide_lite.yaml
If you use atavide light, please cite it and then please also cite the other papers that describe these great tools.