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

Bowtie2 Mapping

Step	Meta-Wrapper	Wrapper
Bowtie2-build	bowtie2-sambamba meta-wrapper	bowtie2-build
Fastp		fastp
Bowtie2-align	bowtie2-sambamba meta-wrapper	bowtie2-align
Sambamba sort	bowtie2-sambamba meta-wrapper	sambamba-sort

┌───────────────────────────┐   ┌─────────────────────────┐
│Genome indexation (Bowtie2)│   │Sequence cleaning (fastp)│
└──────────────┬────────────┘   └────────┬────────────────┘
               │                         │                 
               │                         │                 
┌──────────────▼───────────────┐         │                 
│Short read alignment (Bowtie2)◄─────────┘                 
└──────────────┬───────────────┘                           
               │                                           
               │                                           
┌──────────────▼───────────────────────────┐               
│Sort and compress aligned reads (sambamba)│               
└──────────────────────────────────────────┘               

Filtering

Step	Meta-Wrapper	Wrapper
Sambamba-view	bowtie2-sambamba meta-wrapper	sambamba-view
Sambamba-markdup	bowtie2-sambamba meta-wrapper	sambamba-markdup
Sambamba-index	bowtie2-sambamba meta-wrapper	sambamba-index
Deeptools		deeptools-alignment-sieve

 ┌─────────────────────────┐                                                
 │Aligned reads (see above)│                                                
 └───────────┬─────────────┘                                                
             │                                                              
             │                                                              
             │                                                              
             │                                                              
 ┌───────────▼─────────────────┐                                            
 │Filter low quality (sambamba)│                                            
 └───────────┬─────────────────┘                                            
             │                                                              
             │                                                              
             │                                                              
 ┌───────────▼──────────────┐           ┌──────────────────────────────────┐
 │Mark duplicates (sambamba)├───────────►Index aligned sequences (sambamba)│
 └───────────┬──────────────┘           └─────────┬────────────────────────┘
             │                                    │                         
             ├────────────────────────────────────┘                         
             │                                                              
┌────────────▼─────────────────┐        ┌──────────────────────────────────┐
│ Sieve alignments (deeptools) ├────────►Index aligned sequences (sambamba)│
│     OPTIONAL                 │        │     OPTIONAL                     │
└──────────────────────────────┘        └──────────────────────────────────┘

QC

Step	Wrapper
Picard	picard-collectmultiplemetrics
Samtools	samtools-stats
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)◄─────────────────┘                     
                                └─────────────────────────┘