Uganda MAGs

Pipeline description

This pipeline starts with different individual assemblies (fasta files) and their respective reads (fastq.gz files). It will map all reads against all the assemblies using BWA. Then per sample, Metabat2, Concoct and Metabinner are ran to create genomic bins. These bins are then consolidated using DasTool. After that, the bins of all samples are dereplicated with dRep to form MAGs. CheckM and GtdbTk are then used to estimate the quality and taxonomy of the MAGs

Setup

• Place your preprocessed/trim reads (e.g. sample_R2.fastq.gz and sample_R2.fastq.gz files) in a reads folder
• Place the individual assemblies (e.g. sample.fasta) into an assembly folder
• Modify the config.yaml file to change the different paths and eventually the different options
• Modify the sample_list.txt file to include your samples

Without Slurm

snakemake -rp --cores 28 --use-conda --rerun-incomplete

With Slurm

This part was mainly taken from @susheelbhanu nomis_pipeline

• Modify the slurm.yaml file by checking partition, qos and account that heavily depends on your system
• Modify the sbatch.sh file by checking #SBATCH -p, #SBATCH --qos= and #SBATCH -A options that heavily depends on your system

sbatch config/sbatch.sh