Metagenomics Workflows

Workflows for metagenomic sequence data processing and analysis. Further documentation found in each workflow folder.

Long read assembly has been moved to a new repository: Lathe

Installing workflows

First, install miniconda3

Then install snakemake. This can be done with the following.

conda install snakemake
snakemake --version #please ensure this is >=5.4.3

Next, clone this github directory to some location where it can be stored permanently. Remember to keep it updated with git pull.

git clone https://github.com/elimoss/metagenomics_workflows.git

Snakemake does not have native support for SLURM. Instructions to enable Snakemake to schedule cluster jobs with SLURM can be found at https://github.com/bhattlab/slurm

bin_label_and_evaluate

Snakemake workflow for aligning, binning, classifying and evaluating a metagenomic assembly.

Before running this workflow, please do the following:

source activate mgwf #activate the environment
cd <checkm data directory of your choice>
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz #download checkm databases
tar -zxf checkm_data_2015_01_16.tar.gz
checkm data setRoot #set the location for checkm data and wait for it to initialize

Inputs

Alter config.yaml to provide the following:

Assembly: Sequence to bin. Fasta format.
Sample: names the output directory.
Reads 1, Reads 2: forward and reverse reads in fastq or fastq.gz format.
Krakendb: Kraken2 database with which to classify asssembly contigs.
Read length: read length.

Known problems: occasionally fails after binning step. Just re-run snakemake. This is a problem with dynamic job scheduling, and will hopefully be fixed in a future snakemake update.

to run, please use the following:

snakemake -s path/to/metagenomics_workflows/bin_label_and_evaluate/Snakefile --configfile path/to/modified_config.yaml --restart-times 0 --keep-going
#--profile scg #run this on a cluster.  this is highly recommended.  See above.

assembly_comparison_circos

Snakemake workflow for visualizing assemblies of a particular genome across conditions and time points. Calls out pre-identified sequences, highlights selected contigs.