# EukRecover Pipeline to recover eukaryotic MAGs using CONCOCT, metaBAT2 and EukCC's merging algorythm. Needs paired end shotgun metagenomic reads. ## Environment Eukrecover requires an environment with snakemake and metaWRAP. ## Quickstart Define your samples in the file `samples.csv`. This file needs to have the columns project and run to identify each metagenome. This pipeline does not support co-binning, but feel free to change it. Clone this repro wherever you want to run the pipeline: ``` git clone https://github.com/openpaul/eukrecover/ ``` You can then run the snakemake like so ``` snakemake --use-singularity ``` The pipeline used dockerhub to fetch all tools, so make sure you have singularity installed. ## Prepare databases The pipeline will setup databases for you, but if you already have a EukCC or a BUSCO 5 database you can use them by specifying the location in the file `config/config.yaml` ## Output: In the folder results you will find a folder `MAGs` which will contain a folder `fa` containing the actual MAG fastas. In addition you will find stats for each MAG in the table `QC.csv`. This table contains the following columns: name,eukcc_compl,eukcc_cont,BUSCO_C,BUSCO_M,BUSCO_D,BUSCO_F,BUSCO_tax,N50,bp ## Citation: If you use this pipeline please make sure to cite all used software. For this please reffer to the used rules.