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