/fair_star_mapping

Sanekamke workflow used to align reads with STAR

Primary LanguagePythonMIT LicenseMIT

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Snakemake workflow used to align ungapped reads to the genome with Bowtie2.

Usage

The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.

Results

A complete description of the results can be found here in workflow reports.

Material and Methods

The tools used in this pipeline are described here textually. Web-links are available below:

Index and genome sequences with fair_genome_indexer

See fair_genome_indexer documentation about DNA sequence preparation

Raw-sequences QC with fair_fastqc_multiqc

See fair_fastqc_multiqc documentation about ranw sequences quality controls

STAR Mapping

Step Wrapper
STAR-index star-index-wrapper
STAR-align star-align-wrapper
Sambamba-sort sambamba-sort-wrapper 
┌───────────────────────────┐   ┌─────────────────────────┐
│Genome indexation (STAR)   │   │Sequence cleaning (fastp)│
└──────────────┬────────────┘   └────────┬────────────────┘
               │                         │                 
               │                         │                 
┌──────────────▼───────────────┐         │                 
│Short read alignment (STAR)   ◄─────────┘                 
└──────────────┬───────────────┘                           
               │                                           
               │                                           
┌──────────────▼───────────────────────────┐               
│Sort and compress aligned reads (sambamba)│               
└──────────────────────────────────────────┘

Filtering

Step Wrapper
Sambamba-view sambamba-view
Sambamba-markdup sambamba-markdup
Picard picard-addorreplacegroups
Sambamba-index sambamba-index 
┌──────────────────────────┐        
│Aligned reads (see above) │        
└──────────────┬───────────┘        
               │                    
               │                    
┌──────────────▼──────────────┐     
│Filter low quality (sambamba)│     
└──────────────┬──────────────┘     
               │                    
               │                    
┌──────────────▼───────────┐        
│Mark duplicates (sambamba)│        
└──────────────┬───────────┘        
               │                    
               │                    
┌──────────────▼───────────┐        
│Add read groups (picard)  │        
└──────────────┬───────────┘        
               │                    
               │                    
               │                    
┌──────────────▼───────────────────┐
│Index aligned sequences (sambamba)│
└──────────────────────────────────┘

QC

Step Wrapper
Picard picard-collectmultiplemetrics
Samtools samtools-stats
RSeQC official documentation
RNASeQC official documentation
NGSderive official documentation
Goleft official documentation
MultiQC multiqc-wrapper 
┌──────────────────────┐        ┌─────────────────────┐                ┌─────────────────────────┐
│ Cleaned reads (fastp)│    ┌───┤Duplicates (sambamba)◄────────────────┤Aligned reads (see above)│
└─────────────────────┬┘    │   └─────────────────────┘                └────┬────────────────────┘
                      │     │                                               │                     
                      ├─────┘                                               │                     
                      │         ┌──────────────────────────┐                │                     
                      ├─────────┤Alignment metrics (picard)◄────────────────┤                     
                      │         └──────────────────────────┘                │                     
                      │                                                     │                     
                      │                                                     │                     
                      │         ┌────────────────────────────┐              │                     
                      ├─────────┤Alignment metrics (samtools)◄──────────────┤                     
                      │         └────────────────────────────┘              │                     
                      │                                                     │                     
┌────────────────┐    │                                                     │                     
│ Quality report │    │         ┌─────────────────────────┐                 │                     
│   (multiqc)    ◄────┼─────────┤Alignment metrics (rseqc)◄─────────────────┤                     
└────────────────┘    │         └─────────────────────────┘                 │                     
                      │                                                     │                     
                      │                                                     │                     
                      │         ┌───────────────────────────┐               │                     
                      ├─────────┤Library metrics (ngsderive)◄───────────────┤                     
                      │         └───────────────────────────┘               │                     
                      │                                                     │                     
                      │                                                     │                     
                      │         ┌─────────────────────────┐                 │                     
                      ├─────────┤Coverage metrics (goleft)◄─────────────────┤                   
                      │         └─────────────────────────┘                 │                      
                      │                                                     │                     
                      │         ┌───────────────────────────┐               │                     
                      └─────────┤Alignment metrics (rnaseqc)◄───────────────┘                     
                                └───────────────────────────┘