Analyzing gene flow in the deep biosphere via "multi-omics" integrated analysis.

config/ : configuration files

data/ : raw data goes here

resources/ : databases, references etc.

workflow/ : main directory for the snakemake workflow

data/testdata/ :

This folder contains two small test datasets:

• test

This dataset is comprised of 25k paired-end reads from the SCAPP test data + 25k paired-end reads each from three plasmids:

• CEX4 plasmid pCEX4 (LC556220.1, Enterobacter cloacae)

• unnamed plasmid (NC_012780.1, [Eubacterium] eligens ATCC 27750)

• plasmid pBPSE01 (NZ_KF418775.1, Burkholderia pseudomallei strain MSHR1950) generated using randomreads.sh from bbmap.

• mock

comprised of 50k reads from the minced testdata of the Aquifex aeolicus VF5 genome (generated with randomreads.sh) + 50k reads subsampled from a synthetic mock metagenome (using seqtk).

snakemake --use-conda -j 10 -rpk --profile slurm --configfile config/deepbio_config.yaml

• MetaplasmidSPADES (Antipov et al 2019)
• SCAPP (Pellow et al 2020)
• Recycler (Rozov et al 2016)

• Virsorter (Roux et al 2015)
• MetaviralSPADES (Antipov et al 2020)

• Minced

• Benchmarking shows that assembly + binning underperforms for plasmids and GIs: Maguire et al 2020