atavide lite

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.

Pipeline steps

1. Run fastp to trim Illumina adapters
2. Use minimap2 and samtools to filter out host and not host reads. Currently host reads are ignored. Host can be human or anything else.
3. Use mmseqs easy-taxonomy to compare not host reads to UniRef. By default we use UniRef50 but you could use any version.
4. Create a taxonomic summary for each sample and make a single .tsv file.
5. Connect in the subsystems from BV-BRC, and make a table that includes subsystems and taxonomic information
6. Create a subsystems taxonomy for the data

different versions

See the verions:

• slurm - designed to work on Flinders deepthought infrastructure
• pbs - designed to work on the NCI infrastructrue for now
• minion pawsey

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.