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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

This is 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.
Output:A set of BAM files
Status:draft
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

Installation

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_mapper

Usage

sequana_pipelines_mapper --help
sequana_pipelines_mapper --input-directory DATAPATH

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

cd mapper
sh 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.

Requirements

This pipelines requires the following executable(s):

  • bamtools
  • bwa
  • multiqc
https://raw.githubusercontent.com/sequana/sequana_mapper/master/sequana_pipelines/mapper/dag.png

Details

This pipeline runs mapper in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.

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
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.

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