Description:

sequanamapper 1.2.1

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

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.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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