Package: sequana-mapper
This is themapperpipeline from theSequanaprojetOverview:This is a simple pipeline to map several FastQ files onto a reference using different mappers/alignersInput:A set of FastQ files (illumina, pacbio, etc).Output:A set of BAM files (and/or bigwig) and HTML reportStatus:ProductionDocumentation:This README file, andhttps://sequana.readthedocs.ioCitation:Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOIhttps://doi:10.21105/joss.00352InstallationIf you already have all requirements, you can install the packages using pip:pip install sequana_mapper --upgradeYou will need third-party software such as fastqc. Please see below for details.UsageThis 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-coverageThis 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 runThis 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 usesequanixinterface.RequirementsThis pipelines requires the following executable(s):bamtoolsbwamultiqcsequana_coverageminimap2bowtie2deeptoolsDetailsThis pipeline runsmapperin parallel on the input fastq files (paired or not).
A brief sequana summary report is also produced. When using–pacbiooption,-x map-pboptions 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 detailsHere is thelatest documented configuration fileto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.ChangelogVersionDescription1.2.1fix bwa_split bwa aggreate stage (bug fix)1.2.0Implement a bwa_split method to speed up mapping of very large
fastq files.1.1.0BAM files are now filtered to remove unmapped readsset wrappers branch in config file and update pipeline.refactorise to use click and new sequana-pipetools1.0.0Use latest sequana-wrappers and graphviz apptainer0.12.0Use latest pipetools and add singularity containers0.11.1Fix typo when setting coverage to True and allow untagged filenames0.11.0implement feature counts for capture-seq projects0.10.1remove getlogdir and getname0.10.0use new wrappers framework0.9.0fix issue with logger and increments requirementsadd new option –pacbio to automatically set the options for
pacbio data (-x map-pb and readtag set to None)0.8.13add the thread option in minimap2 case0.8.12factorise multiqc rule0.8.11Implemente the –from-project option and new frameworkcustom HTMrLl report0.8.10change samtools_depth rule and switched to bam2cov to cope with null
coverage0.8.9fix requirements0.8.8fix pipeline rule for bigwig + renamed output_bigwig into
create_bigwig; fix the multiqc config file0.8.7fix config file creation (for bigwig)0.8.6added bowtie2 mapper + bigwig as output, make coverage optional0.8.5create a sym link to the HTML report. Better post cleaning.0.8.4Fixing multiqc (synchronized with sequana updates)0.8.3add sequana_coverage rule.0.8.2add minimap2 mapper0.8.1fix bamtools stats rule to have different output name for multiqc0.8.0First release.Contribute & Code of ConductTo contribute to this project, please take a look at theContributing Guidelinesfirst. Please note that this project is released with aCode of Conduct. By contributing to this project, you agree to abide by its terms.