A multi-sample mapper to map reads onto a reference
Project description
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
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
Version |
Description |
|---|---|
1.2.1 |
|
1.2.0 |
|
1.1.0 |
|
1.0.0 |
|
0.12.0 |
|
0.11.1 |
|
0.11.0 |
|
0.10.1 |
|
0.10.0 |
|
0.9.0 |
|
0.8.13 |
|
0.8.12 |
|
0.8.11 |
|
0.8.10 |
|
0.8.9 |
|
0.8.8 |
|
0.8.7 |
|
0.8.6 |
|
0.8.5 |
|
0.8.4 |
|
0.8.3 |
|
0.8.2 |
|
0.8.1 |
|
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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for sequana_mapper-1.2.1-py3-none-any.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 3d539bbbeef35e5445d7b0006bea72a3848a62ec2e6158082023de0c50b410b7 |
|
| MD5 | de9a34675d0b3cc58151eb6267a9327a |
|
| BLAKE2b-256 | 134999c06e6d2c422843b80a40630a70092c022a424d59fe0a3e5ea9a7055bc4 |
