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MPUSP/snakemake-bacterial-riboseq

Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.

Overview​

Testing: GitHub Actions Workflow Status GitHub Actions Workflow Status

Last update: 2026-04-07

Latest release: v1.6.0

Topics: bioinformatics-pipeline conda riboseq ribosome-profiling singularity snakemake workflow

Authors: @m-jahn @rabioinf

Configuration​

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

Running the workflow​

Input data​

Reference genome​

An NCBI Refseq ID, e.g. GCF_000006945.2. Find your genome assembly and corresponding ID on NCBI genomes. Alternatively use a custom pair of *.fasta file and *.gff file that describe the genome of choice.

Important requirements when using custom *.fasta and *.gff files:

  • *.gff genome annotation must have the same chromosome/region name as the *.fasta file (example: NC_003197.2)
  • *.gff genome annotation must have gene and CDS type annotation that is automatically parsed to extract transcripts
  • all chromosomes/regions in the *.gff genome annotation must be present in the *.fasta sequence
  • but not all sequences in the *.fasta file need to have annotated genes in the *.gff file

Read data​

Ribosome footprint sequencing data in *.fastq.gz format. The currently supported input data are single-end, strand-specific reads. Input data files are supplied via a mandatory table, whose location is indicated in the config.yml file (default: samples.tsv). The sample sheet has the following layout:

sampleconditionreplicatefq1
RPF-RTP1RPF-RTP1data/RPF-RTP1_R1_001.fastq.gz
RPF-RTP2RPF-RTP2data/RPF-RTP2_R1_001.fastq.gz

Some configuration parameters of the pipeline may be specific for your data and library preparation protocol. The options should be adjusted in the config.yml file. For example:

  • Minimum and maximum read length after adapter removal (see option cutadapt: default). Here, the test data has a minimum read length of 15 + 7 = 22 (2 nt on 5'end + 5 nt on 3'end), and a maximum of 45 + 7 = 52.
  • Unique molecular identifiers (UMIs). For example, the protocol by McGlincy & Ingolia, 2017 creates a UMI that is located on both the 5'-end (2 nt) and the 3'-end (5 nt). These UMIs are extracted with umi_tools (see options umi_extraction: method and pattern).

Example configuration files for different sequencing protocols can be found in resources/protocols/.