MPUSP/snakemake-assembly-postprocessing

A Snakemake workflow for the post-processing of microbial genome assemblies.

Overview

Testing:

Last update: 2025-12-10

Latest release: v1.1.0

Topics: apptainer bacteria conda genome-assembly genome-sequencing microbes pipeline postprocessing quality-control snakemake-workflow genomics

Authors: @rabioinf @m-jahn

Configuration

The following configuration details are extracted from the config's README file.

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Workflow overview

A Snakemake workflow for the post-processing of microbial genome assemblies.

1. Parse samples.csv table containing the samples's meta data (python)
2. Annotate assemblies using one of the following tools:
   1. NCBI's Prokaryotic Genome Annotation Pipeline (PGAP). Note: needs to be installed manually
   2. prokka, a fast and light-weight prokaryotic annotation tool
   3. bakta, a fast, alignment-free annotation tool. Note: Bakta will automatically download its companion database from zenodo (light: 1.5 GB, full: 40 GB)
3. Create a QC report for the assemblies using Quast
4. Create a pangenome analysis (orthologs/homologs) using Panaroo

Running the workflow

Input data

This workflow requires fasta input data. The samplesheet table has the following layout:

sample	species	strain	id_prefix	file
EC2224	"Streptococcus pyogenes"	SF370	SPY	assembly.fasta
...	...	...	...	...

Note: Pangenome analysis with Panaroo requires at least two samples.

Parameters

This table lists all parameters that can be used to run the workflow.

Parameter	Type	Details	Default
samplesheet	string	Path to the sample sheet file in csv format
tool	array[string]	Annotation tool to use (one of prokka, pgap, bakta)
pgap		PGAP configuration object
bin	string	Path to the PGAP script
use_yaml_config	boolean	Whether to use YAML configuration for PGAP	False
prepare_yaml_files		Paths to YAML templates for PGAP
generic	string	Path to the generic YAML configuration file
submol	string	Path to the submol YAML configuration file
prokka		Prokka configuration object
center	string	Center name for Prokka annotation (used in sequence IDs)
extra	string	Extra command-line arguments for Prokka	--addgenes
bakta		Bakta configuration object
download_db	string	Bakta database type (full, light, or none)	light
existing_db	string	Path to an existing Bakta database (optional). Needs to be combined with download_db='none'	--keep-contig-headers --compliant
extra	string	Extra command-line arguments for Bakta
quast		QUAST configuration object
reference_fasta	string	Path to the reference genome for QUAST
reference_gff	string	Path to the reference annotation for QUAST
extra	string	Extra command-line arguments for QUAST
panaroo		Panaroo configuration object
remove_source	string	Source types to remove in Panaroo (regex supported)	cmsearch
remove_feature	string	Feature types to remove in Panaroo (regex supported)	tRNA|rRNA|ncRNA|exon|sequence_feature
extra	string	Extra command-line arguments for Panaroo	--clean-mode strict --remove-invalid-genes