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.