Sequana: a set of NGS pipelines

This page serves as an additional set of resources for the Sequana project. Sequana is comprised of a Python library, the documentation of which is accessible on Read The Docs. The source code for the Python library can be found on GitHub. If you use Sequana, please cite: Cokelaer et al., Journal of Open Source Software, 2017 (doi:10.21105/joss.00352).   JOSS paper

One of the primary objective of the Sequana project is to offer a collection of NGS pipelines. The pipelines currently available are located on PyPI and the Sequana GitHub organisation page, each having their own repository. For instance, the RNA-seq pipeline can be found at sequana/rnaseq.

This page is also a place for providing supplementary information to the main repositories.

Pipelines

Sequana provides a collection of NGS pipelines. Each pipeline lives in its own repository on the Sequana GitHub organisation. Below are some highlighted pipelines:

sequana_fastqc pipeline overview
sequana_fastqc
A quality-control pipeline that runs FastQC and MultiQC on raw FASTQ files to assess sequencing quality.
🔗 GitHub 📖 README GitHub stars 📄 Report
sequana_rnaseq pipeline overview
sequana_rnaseq
An RNA-seq pipeline that covers trimming, alignment, feature counting, and differential expression analysis.
🔗 GitHub 📖 README GitHub stars 📄 Report
sequana_variant_calling pipeline overview
sequana_variant_calling
A variant-calling pipeline that performs read trimming, alignment, and SNP/indel detection using standard tools such as BWA and freebayes, with interactive HTML reports.
🔗 GitHub 📖 README GitHub stars 📄 Report
sequana_lora pipeline overview
sequana_lora
A long-read assembly pipeline for Oxford Nanopore (and PacBio) data that performs basecalling, quality control, de-novo assembly, polishing, and assembly quality assessment with tools such as Flye, Medaka, and BUSCO.
🔗 GitHub 📖 README GitHub stars 📄 Report
sequana_multitax pipeline overview
sequana_multitax
A taxonomic classification pipeline that runs multiple classifiers (Kraken2, Centrifuge, etc.) on sequencing reads, merges results, and produces comparative summary reports.
🔗 GitHub 📖 README GitHub stars
sequana_demultiplex pipeline overview
sequana_demultiplex
A demultiplexing pipeline built around bcl2fastq / bcl-convert that converts Illumina BCL files into FASTQ files, validates sample sheets, and generates MultiQC summary reports.
🔗 GitHub 📖 README GitHub stars 📄 Report
sequana_hic pipeline overview
sequana_hic
A Hi-C pipeline for chromatin conformation capture data that performs read trimming, alignment, contact-map generation, and quality assessment of 3D genome organisation.
🔗 GitHub 📖 README GitHub stars
sequana_chipseq pipeline overview
sequana_chipseq
A ChIP-seq pipeline that covers read trimming, alignment, peak calling, and downstream annotation to identify protein–DNA binding sites and histone modifications.
🔗 GitHub 📖 README GitHub stars
sequana_denovo pipeline overview
sequana_denovo
A de-novo assembly pipeline for short-read Illumina data that performs trimming, assembly, scaffolding, and assembly quality assessment with tools such as SPAdes and QUAST.
🔗 GitHub 📖 README GitHub stars

These are just a few highlights. Sequana encompasses many more pipelines — both public and private — covering a wide range of sequencing applications. A broader overview is available on github.com/sequana/sequana, the Sequana GitHub organisation, and the full documentation at sequana.readthedocs.io.

Tools & Standalone Applications

Sequana ships published tools and a set of standalone sub-commands invocable directly from the command line (sequana <subcommand>), all distributed as part of the sequana Python package.

Sequana Coverage — genome depth-of-coverage analysis (GigaScience 2018 Fig. 1)
Sequana Coverage
Published in GigaScience — DOI: 10.1093/gigascience/giy110
Fast detection of genomic regions with abnormal depth of coverage. Models coverage with a mixture of distributions, highlights deletions, duplications, and low-complexity regions, and produces interactive HTML reports.
🔗 GitHub 📖 Docs
Sequanix — desktop GUI for Snakemake pipelines
Sequanix
Published in Bioinformatics — DOI: 10.1093/bioinformatics/bty034
Desktop GUI (PyQt5) for configuring and executing Snakemake pipelines without writing code. Dynamically renders widgets from config files and monitors pipeline progress in real time.
🔗 GitHub 📖 Docs
sequana taxonomy
Taxonomic classification of reads using Kraken2, with summary plots for metagenomics studies.
📖 Docs
sequana summary
Summary statistics (read counts, GC content, quality metrics) for FASTQ files without running a full pipeline.
📖 Docs
sequana enrichment
Gene Ontology and KEGG pathway enrichment analysis on differentially expressed genes, with interactive visualisations.
📖 Docs
sequana samplesheet
Validate and convert Illumina sample-sheet files, catching formatting errors before demultiplexing.
📖 Docs
sequana gtf_fixer
Fix common inconsistencies in GTF/GFF annotation files so they are compatible with downstream RNA-seq tools.
📖 Docs

Talks

Web Applications

Check your Illumina Sample Sheet

Report examples (click on the image)

The following was generated with the Sequana Coverage standalone application and keep here a it is reference in other places. This is the coverage along a virus genome where the black dot line represent the coverage, the blue is the median coverage, and red lines are the top and bottow thresholds for detecting event of interest.