This is the mapper pipeline from the Sequana projet

Overview:	This is a simple pipeline to map several FastQ files onto a reference using different mappers/aligners
Input:	A set of FastQ files (illumina, pacbio, etc).
Output:	A set of BAM files (and/or bigwig) and HTML report
Status:	Production
Documentation:	This README file, and https://sequana.readthedocs.io
Citation:	Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352

Installation

If you already have all requirements, you can install the packages using pip:

pip install sequana_mapper --upgrade

You will need third-party software such as fastqc. Please see below for details.

Usage

Scan FastQ files in a directory and set up the pipeline (replace DATAPATH and genome.fa with your inputs):

sequana_mapper --input-directory DATAPATH --reference-file genome.fa --aligner-choice bwa
sequana_mapper --input-directory DATAPATH --reference-file genome.fa --aligner-choice bwa --do-coverage
sequana_mapper --input-directory DATAPATH --reference-file genome.fa --aligner-choice bwa --create-bigwig

For long-read data, use the dedicated presets:

sequana_mapper --input-directory DATAPATH --reference-file genome.fa --pacbio     # sets minimap2 -x map-pb
sequana_mapper --input-directory DATAPATH --reference-file genome.fa --nanopore   # sets minimap2 -x map-ont

For capture-seq projects (feature counting):

sequana_mapper --input-directory DATAPATH --reference-file genome.fa --capture-annotation-file targets.saf

This creates a mapper/ directory with the pipeline and configuration file. Execute the pipeline locally:

cd mapper
sh mapper.sh

See .sequana/profile/config.yaml to tune Snakemake behaviour (cores, cluster settings, etc.).

Usage with apptainer

With apptainer, initiate the working directory as follows:

sequana_mapper --input-directory DATAPATH --reference-file genome.fa --use-apptainer

Images are downloaded in the working directory but you can store them in a shared location:

sequana_mapper --input-directory DATAPATH --reference-file genome.fa --use-apptainer --apptainer-prefix ~/.sequana/apptainers

and then:

cd mapper
sh mapper.sh

Requirements

This pipeline requires the following executables (install via bioconda/conda):

• bwa — short-read aligner (default)
• minimap2 — long-read aligner (PacBio / Nanopore)
• bowtie2 — alternative short-read aligner
• samtools / sambamba — BAM processing
• bamtools — BAM statistics
• deeptools — bigwig generation (bamCoverage)
• bedtools — genome arithmetic
• subread — feature counting (featureCounts, capture-seq only)
• mosdepth — fast coverage depth
• seqkit — FASTQ statistics
• multiqc — aggregated HTML report
• sequana_coverage — coverage analysis (prokaryotes)

Install all dependencies at once:

mamba env create -f environment.yml

Details

This pipeline maps FastQ files (paired or single-end) in parallel onto a reference genome and produces filtered BAM files, a MultiQC HTML report, and optionally coverage tracks and feature counts.

Aligner choice (--aligner-choice):

• bwa (default) — BWA-MEM; index algorithm is auto-selected (is or bwtsw) based on reference size
• bwa_split — experimental; splits large FastQs into 1 M-read chunks for parallel BWA jobs, then merges
• minimap2 — long-read aligner; use --pacbio (sets -x map-pb) or --nanopore (sets -x map-ont)
• bowtie2 — standard short-read aligner

BAM filtering: unmapped reads are removed to minimise file size. Statistics reported by MultiQC (in {sample}/bamtools_stats/) still include both mapped and unmapped read counts.

Optional outputs:

• --do-coverage — runs sequana_coverage for depth-of-coverage analysis (prokaryotes)
• --create-bigwig — generates bigwig files via bamCoverage (deeptools)
• --capture-annotation-file — enables featureCounts for capture-seq efficiency metrics

Rules and configuration details

Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.

Changelog

Version	Description
1.4.1	update to use wrappers.shells and wrappers.snippets drop wrappers usage
1.4.0	update wrappers to v24.8.29 update sequana_pipetools requirement to >=1.5
1.3.1	remove temp on BWA BAM file (more practical to keep them)
1.3.0	uses new sequana_coverage wrapper
1.2.1	fix bwa_split bwa aggreate stage (bug fix)
1.2.0	Implement a bwa_split method to speed up mapping of very large fastq files.
1.1.0	BAM files are now filtered to remove unmapped reads set wrappers branch in config file and update pipeline. refactorise to use click and new sequana-pipetools
1.0.0	Use latest sequana-wrappers and graphviz apptainer
0.12.0	Use latest pipetools and add singularity containers
0.11.1	Fix typo when setting coverage to True and allow untagged filenames
0.11.0	implement feature counts for capture-seq projects
0.10.1	remove getlogdir and getname
0.10.0	use new wrappers framework
0.9.0	fix issue with logger and increments requirements add new option --pacbio to automatically set the options for pacbio data (-x map-pb and readtag set to None)
0.8.13	add the thread option in minimap2 case
0.8.12	factorise multiqc rule
0.8.11	Implemente the --from-project option and new framework custom HTMrLl report
0.8.10	change samtools_depth rule and switched to bam2cov to cope with null coverage
0.8.9	fix requirements
0.8.8	fix pipeline rule for bigwig + renamed output_bigwig into create_bigwig; fix the multiqc config file
0.8.7	fix config file creation (for bigwig)
0.8.6	added bowtie2 mapper + bigwig as output, make coverage optional
0.8.5	create a sym link to the HTML report. Better post cleaning.
0.8.4	Fixing multiqc (synchronized with sequana updates)
0.8.3	add sequana_coverage rule.
0.8.2	add minimap2 mapper
0.8.1	fix bamtools stats rule to have different output name for multiqc
0.8.0	First release.

Contribute & Code of Conduct

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.