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A simple mapper to map reads onto a reference. This is useful for quick QCs and also secondary analysis

Project description JOSS (journal of open source software) DOI

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
Citation:Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352


You must install Sequana first (use –upgrade to get the latest version installed):

pip install sequana --upgrade

Then, just install this package:

pip install sequana_mapper --upgrade


sequana_mapper --input-directory DATAPATH  --mapper bwa --create-bigwig
sequana_mapper --input-directory DATAPATH  --mapper bwa --do-coverage

This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:

cd mapper
sh  # for a local run

This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:

snakemake -s mapper.rules -c config.yaml --cores 4 --stats stats.txt

Or use sequanix interface.


This pipelines requires the following executable(s):

  • bamtools
  • bwa
  • multiqc
  • sequana_coverage
  • minimap2
  • bowtie2
  • deeptools


This pipeline runs mapper in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced. When using –pacbio option, -x map-pb options is automatically added to the config.yaml file and the readtag is set to None.

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.


Version Description
  • implement feature counts for capture-seq projects
  • remove getlogdir and getname
  • use new wrappers framework
  • 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)
  • add the thread option in minimap2 case
  • factorise multiqc rule
  • Implemente the –from-project option and new framework
  • custom HTMrLl report
  • change samtools_depth rule and switched to bam2cov to cope with null coverage
  • fix requirements
  • fix pipeline rule for bigwig + renamed output_bigwig into create_bigwig; fix the multiqc config file
  • fix config file creation (for bigwig)
  • added bowtie2 mapper + bigwig as output, make coverage optional
  • create a sym link to the HTML report. Better post cleaning.
  • Fixing multiqc (synchronized with sequana updates)
  • add sequana_coverage rule.
  • add minimap2 mapper
  • 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.

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Source Distribution

sequana_mapper-0.11.0.tar.gz (47.5 kB view hashes)

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