Pipelines#

Sequana ships a family of NGS pipelines, each in its own GitHub repository and PyPI package. They share a common installation pattern, CLI shape, and HTML report layout.

Quick start #

pip install sequana_<name> --upgrade
sequana_<name> --help

For example:

pip install sequana_fastqc --upgrade
sequana_fastqc --input-directory my_data
cd fastqc && sh fastqc.sh

The configuration file config.yaml lives next to the snakefile in the working directory and can be edited before launch. See Pipeline user guide for a walkthrough of the common options.

Containers #

Every Sequana pipeline ships an apptainers.yaml pointing at the matching damona image. Pull them on demand with:

sequana_<name> ... --use-apptainer

This is the recommended way to avoid conda / system tool clashes.

Pipeline catalogue #

Quality control #

Pipeline	Description	Repository
`sequana_fastqc`	Sequencing quality control (FastQC + MultiQC).	sequana/fastqc
`sequana_pacbio_qc`	PacBio long-read quality control.	sequana/pacbio_qc
`sequana_ribofinder`	Estimate ribosomal content of a sample.	sequana/ribofinder

Mapping and coverage #

Pipeline	Description	Repository
`sequana_mapper`	Map reads onto a target genome (bowtie2 / bwa / minimap2).	sequana/mapper
`sequana_multicov`	Multi-sample coverage analysis.	sequana/multicov

Variants and RNA-seq #

Pipeline	Description	Repository
`sequana_variant_calling`	Variant calling (freebayes + snpEff + coverage).	sequana/variant_calling
`sequana_rnaseq`	Full RNA-seq pipeline (alignment, counts, DESeq2 report).	sequana/rnaseq

Long-read pipelines #

Pipeline	Description	Repository
`sequana_lora`	Map long reads onto a target genome.	sequana/lora
`sequana_nanomerge`	Merge barcoded (or unbarcoded) Nanopore FASTQ files + report.	sequana/nanomerge
`sequana_laa`	Long-read amplicon analysis.	sequana/laa

Taxonomy and assembly #

Pipeline	Description	Repository
`sequana_multitax`	Taxonomic profiling of multiple samples.	sequana/multitax
`sequana_denovo`	De-novo assembly (digital normalisation + assembler + QC).	sequana/denovo

Utilities #

Pipeline	Description	Repository
`sequana_demultiplex`	Demultiplex raw Illumina runs (bcl2fastq / bcl-convert).	sequana/demultiplex
`sequana_downsampling`	Downsample FASTQ/BAM files.	sequana/downsampling
`sequana_depletion`	Remove or select reads mapping a reference.	sequana/depletion
`sequana_revcomp`	Reverse-complement sequence data.	sequana/revcomp
`sequana_trf`	Tandem repeats finder wrapper.	sequana/trf

For the complete and always-up-to-date list see the sequana GitHub organisation.

Pipeline reference pages #

A handful of pipelines have a dedicated page in this manual. They embed the README of the corresponding repository via the sequana_pipeline Sphinx directive.

Each pipeline is distributed as sequana_<name> (PyPI) and installs a console script named sequana_<name>. For historical pipelines also exposed as standalone tools (sequana_coverage), the pipeline form is sequana_pipelines_<name> to disambiguate.