tdayris / fair_star_mapping

Sanekamke workflow used to align reads with STAR

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)◄───────────────┘                     
                                └───────────────────────────┘