MPUSP/snakemake-simple-mapping

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

Overview

Testing:

Last update: 2025-12-18

Latest release: v1.5.0

Topics: bowtie2 bwa-mem2 genomics mapping next-generation-sequencing snakemake snakemake-workflow star-alignment variant-calling

Authors: @m-jahn

Configuration

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

---

Workflow overview

This workflow is a best-practice workflow for mapping of reads to reference genomes, minimalistic and simple.

It will attempt to map reads to the reference using one of the included mappers, report read and experiment statistics, create coverage profiles, quantify variants (such as SNPs) using two different tools, and predict the effect of these variants. All of this is performed with minimal input and without lookups to external databases (e.g. for variant effects), which makes the workflow ideal for bacteria and other low-complexity non-model organisms.

The workflow is built using snakemake and consists of the following steps:

1. Download genome reference from NCBI (ncbi tools), or use manual input (fasta, gff format)
2. Check quality of input read data (FastQC)
3. Trim adapters and apply quality filtering (fastp)
4. Map reads to reference genome using:
   1. (Bowtie2)[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml] or
   2. (BWA-MEM2)[https://github.com/bwa-mem2/bwa-mem2] or
   3. (STAR)[https://github.com/alexdobin/STAR]
   4. (minimap2)[https://github.com/lh3/minimap2]
5. Determine experiment type, get mapping stats (rseqc)
6. Generate bigwig or bedgaph coverage profiles (deeptools)
7. Quantify variations and SNPs (bcftools, freebayes)
8. Predict effect of variants such as premature stop codons (VEP or SnpEff)
9. Create consensus of variants and create a visual report (R markdown)
10. Collect statistics from tool output (MultiQC)

Running the workflow

Input data

The workflow requires sequencing data in *.fastq.gz format, and a reference genome to map to. The sample sheet listing read input files needs to have the following layout:

sample	description	read1	read2
sample1	strain XY	sample1_R1.fastq.gz	sample1_R2.fastq.gz
...	...	...	...

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 in tsv format
get_genome
database	string	database to use for genome retrieval, 'ncbi' or 'manual'	ncbi
assembly	string	Refseq ID to use for genome retrieval	GCF_000307535.1
fasta	string	path to a custom FASTA file (optional)
gff	string	path to a custom GFF file (optional)
gff_source_type	array	mapping of GFF source types to feature types
fastp
extra	string	additional arguments to Fastp
mapping
tool	string	mapping tool to use, one of 'bowtie2', 'bwa_mem2'	bwa_mem2
bowtie2
index	string	additional arguments to bowtie build
extra	string	additional arguments to bowtie align
bwa_mem2
extra	string	additional arguments to bwa-mem2
sort	string	sorting tool to use	samtools
sort_order	string	sorting order to use	coordinate
sort_extra	string	additional arguments to the sorting tool
samtools_sort
extra	string	additional arguments to Samtools sort	-m 4G
index	object	Samtools index options
extra	string	additional arguments to Samtools index
star
index	string	additional arguments to STAR index
extra	string	additional arguments to STAR align
minimap2
index	string	additional arguments to minimap2 index
extra	string	additional arguments to minimap2 align	-ax map-ont
sorting	string	sorting order to use	coordinate
sort_extra	string	additional arguments to the sorting tool
mapping_stats
gffread
extra	string	additional arguments to GFFread
rseqc_infer_experiment
extra	string	additional arguments to RSeQC infer_experiment
rseqc_bam_stat
extra	string	additional arguments to RSeQC bam_stat
deeptools_coverage
genome_size	integer	genome size in base pairs	1000
extra	string	additional arguments to DeepTools bamCoverage
variant_calling
bcftools_pileup
uncompressed	boolean	whether to output uncompressed BCF files	False
extra	string	additional arguments to BCFtools pileup
bcftools_call
uncompressed	boolean	whether to output uncompressed VCF files	False
caller	string	use '-c' for consensus or '-m' for multiallelic	-c
extra	string	additional arguments to BCFtools view
bcftools_view
extra	string	additional arguments to BCFtools call
bcftools_filter
filter	string	expression by which to filter BCF/VCF result	-e 'ALT=\".\"'
extra	string	additional arguments to BCFtools filter
freebayes
extra	string	additional arguments to Freebayes call
variant_annotation
tool	string	annotation tool to use, one of 'vep', 'snpeff'	vep
vep
convert_gff	boolean	whether to convert NCBI GFF to Ensemble style GFF	True
plugins	array	VEP plugins to use	[]
extra	string	additional arguments to VEP	see config.yml
snpeff
extra	string	additional arguments to SnpEff	see config.yml
qc
fastqc
extra	string	additional arguments to FastQC
multiqc
extra	string	additional arguments to MultiQC