Snakemake workflow used to align ungapped reads to the genome with Bowtie2.
The usage of this workflow is described in the Snakemake workflow catalog it is also available locally on a single page.
A complete description of the results can be found here in workflow reports.
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
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)│
└──────────────────────────────────────────┘
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)│
└──────────────────────────────────┘
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)◄───────────────┘
└───────────────────────────┘