`atavide` is a complete workflow for metagenomics data analysis, including QC/QA, optional host removal, assembly and cross-assembly, and individual read based annotations. We have also built in some advanced analytics including tools to assign annotations from reads to contigs, and to generate metagenome-assembled genomes in several different ways, giving you the power to explore your data! `atavide` is 100% snakemake and conda, so you only need to install the snakemake workflow, and then everything else will be installed with conda. Steps: 1. QC/QA with [prinseq++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus) 2. optional host removal using bowtie2 and samtools, [as described previously](https://edwards.flinders.edu.au/command-line-deconseq/). To enable this, you need to provide a path to the host db and a host db. Metagenome assembly 1. pairwise assembly of each sample using [megahit](https://github.com/voutcn/megahit) 2. extraction of all reads that do not assemble using samtools flags 3. assembly of all unassembled reads using [megahit](https://github.com/voutcn/megahit) 4. compilation of _all_ contigs into a single unified set using [Flye](https://github.com/fenderglass/Flye) 5. comparison of reads -> contigs to generate coverage MAG creation 1. [metabat](https://bitbucket.org/berkeleylab/metabat/src/master/) 2. [concoct](https://github.com/BinPro/CONCOCT) 3. Pairwise comparisons using [turbocor](https://github.com/dcjones/turbocor) followed by clustering Read-based annotations 1. [Kraken2](https://ccb.jhu.edu/software/kraken2/) 2. [singlem](https://github.com/wwood/singlem) 3. [SUPER-focus](https://github.com/metageni/SUPER-FOCUS) 4. [FOCUS](https://github.com/metageni/FOCUS) Want something else added to the suite? File an issue on github and we'll add it ASAP! ### Installation You will need to install 1. The NCBI taxonomy database somewhere 2. The superfocus databases somewhere, and set the SUPERFOCUS_DB environmental variable Everything else should install automatically.