sequana-mapper 1.2.1

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

This command will scan all files ending in .fastq.gz found in the local directory, create a directory called mapper/ where a snakemake pipeline can be executed.:

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 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 \
    --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/

Or use sequanix interface.

Requirements

This pipelines requires the following executable(s):

• bamtools

• bwa

• multiqc

• sequana_coverage

• minimap2

• bowtie2

• deeptools

Details

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.

The BAM files are filtered to remove unmapped reads to keep BAM files to minimal size. However, the multiqc and statistics to be found in {sample}/bamtools_stats/ includes mapped and unmapped reads information. Each BAM file is stored in a directory named after the sample.

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

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.