Sequana documentation

0.24.2

SEQUANA

How to cite:

Citations are important for us to carry on developments. For Sequana library (including the pipelines), please use

Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352

For the genome coverage tool (sequana_coverage): Desvillechabrol et al, 2018: detection and characterization of genomic variations using running median and mixture models. GigaScience, 7(12), 2018. https://doi.org/10.1093/gigascience/giy110

For Sequanix: Desvillechabrol et al. Sequanix: A Dynamic Graphical Interface for Snakemake Workflows Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034 Also available on bioRxiv (DOI: https://doi.org/10.1101/162701)

🔧 Overview and Installation

Sequana is a Python library dedicated to bioinformatics. It is also a project that includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. We also ship Sequanix, a graphical user interface for Snakemake pipelines.

Pipelines and related projects

Here is a non-exhaustive list of tools and pipelines from the project, with users and developers audience.

name/github	description	Latest Pypi version	Test passing	apptainers
sequana_pipetools	Create and Manage Sequana pipeline			Not required
sequana-wrappers	Set of wrappers to build pipelines			Not required
demultiplex	Demultiplex your raw data			License restriction
denovo	denovo sequencing data
fastqc	Get Sequencing Quality control
LORA	Map sequences on target genome
mapper	Map sequences on target genome
nanomerge	Merge barcoded (or unbarcoded) nanopore fastq and reporting
pacbio_qc	Pacbio quality control
ribofinder	Find ribosomal content
rnaseq	RNA-seq analysis
variant_calling	Variant Calling
multicov	Coverage (mapping)
laa	Long read Amplicon Analysis
revcomp	reverse complement of sequence data
downsampling	downsample sequencing data			Not required
depletion	remove/select reads mapping a reference

Pipelines not yet released

name/github	description	Latest Pypi version	Test passing
trf	Find repeats
multitax	Taxonomy analysis

Please see the documentation for an up-to-date status and documentation.

Contributors

Maintaining Sequana would not have been possible without users and contributors. Each contribution has been an encouragement to pursue this project. Thanks to all:

Changelog :memo:

Version	Description
0.24.2	NEW: Phylogenetic analysis modules (phylo.py, alignment.py) Parse and manipulate Newick trees; MSA parsing (PHYLIP, Stockholm, Nexus, FASTA); consensus sequences and alignment statistics NEW: UpSetPlot visualization library for set intersections NEW: Protein 3D structure analysis (pdb.py) Pipeline catalogue expanded with 7 new pipelines
0.24.1	Fix bowtie2 plots being empty when built from the multiqc plot data files (mqc_bowtie2_{se,pe}_plot_1.txt), whose columns are named after the plot legend. Missing columns now raise instead of drawing an empty figure. Restyle the sidebar of the HTML reports: card layout, hover and active section highlighting, responsive below 900px.
0.24.0	NEW: minor_groove_width module predicting the DNA minor groove width with the DNAshape pentamer model NEW: metrics gains compute_curvature (intrinsic curvature of the helix axis, roll-vector model) and compute_sidd (stress-induced duplex destabilization profile) UPDATE: DNA.plot_tracks replaces the hardcoded plot_all_skews panels. Any combination of tracks can be plotted now. UPDATE: somy module computes IGE/IAL metrics (genome expansion and aneuploidy level per isolate), also saved by sequana somy_score Fix multiqc featureCounts parsing (column names differ between multiqc versions and input files)
0.23.0	NEW: repeats sub package with non B-DNA modules. we also moved repeat- related modules in it (e.g. repeats.py) UPDATE: kozak module with cavener rule and ConsensusBuilder UPDATE: iem module updated to include bcl convert support.
0.22.0	Fix salmon argument handlind, Fix kraken analysis workflow, blast table in kraken report, unclassified file creation. add json export to sequana summary, kozakscore to kozak module. Fix html-report on empty VCF (no variant) raising StopIteration.
0.21.2	Update LAA to use the new variant class
0.21.1	Fix bowti2 plot( multiqc parsing)
0.21.0	Kozak: add plot_logo_bits method (information content / bits scaling) Telomere: refactored sliding window, new annotated plot, cleaner API; telomark CLI gains --plot-style option KEGG enrichment: replace selenium with REST API + PIL rendering FastQ: optimised select_reads_in_list (avoid decode overhead) modules_report: remove deprecated SummaryModule classes
0.20.0	Refactoring FASTA and GFF3 modules/classes (less memory). can now handle large eukaryotes as well. Update Kozak module
0.19.6	NEW add gff command rename and improve the add_CDS function in GFF class BUG fix typo in the is_telomeric function BUG Fix regression in kraken analysis
0.19.5	add embl2fasta, fix CDS parents in GFF file
0.19.4	improved TRF module. NEW: added fastq_split and html_report commands. The latter should be used in the future for sequana pipeline HTML reports. Right now, handles VCF file only.
0.19.3	Fixes plotly issue in RNAdiff plot (#872)
0.19.2	NEW new modules related to genomic metrics (zdna, imotif, cruciform,etc) NEW new visualisation tools NEW parser for hmmtools
0.19.1	update pyproject with matploblib, scipy, and all dependencie except snakemake (keep <8.X and its pulp dependency <2.8) because 8.X breaks the containers and therefore all pipelines. no workaround. we will need a snakemake 'frozen library'. This is unfortunate. CHANGES: remove multiqc plugin quality_control (obsolet) and updated many plugin due to increased version ofmultiqc.
0.19.0	UPDATE pyproject layout to be poetry2.0 compatible. drop support py3.8 NEW: kozak module, somy score, telomere, biomol, rnafold, restriction enzyme UPDATES: sequence module has more metrics (e.g. karlin signature), fastq has a histogram for long reads,
0.18.0	NEW: somy scores (module and standalone) CHANGES: coverage now uses mosdepth for the bam2cov. can also handle creation of the 4-column coverage file from BAM on the fly. Drop python 3.8 support (more and more dependencies issues)
0.17.3	CHANGES: fix sequana/rnaseq#45 to better handle multiqc files especially, feature counts plugin. Fix #855 to be able to name batch effect column arbitrary to any name. Fix batch effect column (and all others) to be strings rather than integer. If integer, factor are sorted based on the integer values, not the factor itself. NEWS: add size factor comments and table.
0.17.2	Pin down pulp<2.8 and snakemake to <8.0 (too many changes in snakemake)
0.17.1	NEW: tsne plot CHANGES: update iem module with additional specs
0.17.0	CHANGE. remove the substractor utility (use sequana_depletion pipeline instead) CHANGE. remove get_max_gc_correlation function from bedtools. not used. CHANGE. Got rid of freebayes_bcf_filter redundant with freebayes_vcf_filter; replace scipy fisher test with own implementation. Remove useless VCF code. FIXES. rnadiff HTML report IMPROV. speedup kegg enrichment using multiprocess IMPROV. sequana_taxonomy can now download toydb and viruses_masking DBs from zenodo NEW function to retrieve the GO terms and genes from panther website NEW keep_reads function in fastq class Major update of the IEM module (renamed IEM class into SampleSheet) NEW addW find-integrated-genes standalone
0.16.9	Major fix on PCA and add batch effect plots in RNAdiff analysis count matrix and DESeq2 output files' headers fixed with missing index (no impact on analysis but only for those willing to use the CSV files in excel) Taxonomy revisited to save taxonomy.dat in gzipped CSV format.
0.16.8	update IEM for more testing better handling of error in RNADiff Add new methods for ribodesigner
0.16.7	Stable release (fix doc), deprecated.
0.16.6	Refactor IEM to make it more robust with more tests.
0.16.5	refactor to use pyproject instead of setuptools remove pkg_resources (future deprecation) remove unused requirements (cookiecutter, adjusttext, docutuils, mock, psutil, pykwalify) cleanup resources (e.g. moving canvas/bar.py into viz)
0.16.4	hot fixes on RNAdiff reports and enrichments
0.16.3	Remove all rules (see sequana/sequana-wrappers) instead add precommit for developers and applied to all modules and doc Fix wrong import for sequana standalone (regression)
0.16.2	save coverage PNG image (regression) Update taxonomy/coverage standalone (regression) and more tests
0.16.1	hotfix missing module
0.16.0	add mpileup module homogenization enrichment + fixup rnadiff Complete refactoring of sequana coverage module. Allow sequana_coverage to handle small eukaryotes in a more memory efficient way. use click for the sequana_taxonomy and sequana_coverage and sequana rnadiff command Small fixup on homer, idr and phantom modules (for chipseq pipeline)
0.15.4	add plot for rnaseq/rnadiff
0.15.3	add sequana.viz.plotly module. use tqdm in bamtools module KEGG API changed. We update sequana to use headless server and keep the feature of annotated and colored pathway. Various improvements on KEGG enrichment including saving pathways, addition --comparison option in sequana sub-command, plotly plots, etc
0.15.2	ribodesigner can now accept an input fasta with no GFF assuming the fasta already contains the rRNA sequences Fix IEM module when dealing with double indexing Fix anchors in HTML reports (rnadiff module) refactorise compare module to take several rnadiff results as input enrichment improvements (export KEGG and GO as csv files
0.15.1	Fix creation of images directory in modules report add missing test related to gff Fix #804
0.15.0	add logo in reports RNADiff reports can now use shrinkage or not (optional) remove useless rules now in sequana-wrappers update main README to add LORA in list of pipelines Log2FC values are now shrinked log2FC values in volcano plot and report table. "NotShrinked" columns for Log2FC and Log2FCSE prior shrinkage are displayed in report table.
0.14.6	add fasta_and_gff_annotation module to correct fasta and gff given a vcf file. add macs3 module to read output of macs3 peak detector. add idr module to read results of idr analysis add phantom module to compute phantom peaks add homer module to read annotation files from annotatePeaks
0.14.5	move start_pipeline standalone in sequana/sequana_pipetools update snpeff module to allows build command to have options
0.14.4	hotfix bug on kegg colorised pathways Fix the hover_name in rnadiff volcano plot to include the index/attribute. pin snakemake to be >=7.16
0.14.3	new fisher metric in variant calling; support several features in rnaseq/rnadiff pin several libaries due to regression during installs
0.14.2	Update ribodesigner
0.14.1	Kegg enrichment improvements; new uniprot module for GO term enrichment
0.14.0	pinned click>=8.1.0; ribodesigner new plots, clustering and notebook
0.13.X	Remove useless standalones or moved to main sequana command Move sequana_lane_merging into a subcommand (sequana lane_merging) General cleanup of documentation, test and links to pipelines add new ribodesigner subcommand
0.12.X	remove some rules now in sequana/sequana-wrappers refactorisation of VCF tools/modules to use vcfpy instead of pyVCF complete change log before 0.12.4 in the github /doc/Changelog.txt

Any :question: Feel free to [open an issue](sequana/sequana#issues)

What is Sequana?

Sequana is a versatile bioinformatics tool that provides:

1. A Python library dedicated to NGS analysis (file-format wrappers, plots, coverage, taxonomy, enrichment, RNA-seq, …).

2. A family of pipelines based on Snakemake, each living in its own GitHub repository.

3. A set of standalone applications:

   1. sequana_coverage — genome coverage analysis with confidence intervals.

   2. sequana_taxonomy — quick taxonomy on a FastQ file (Kraken + Krona).

   3. ~30 other utility sub-commands grouped under the top-level sequana CLI (see Applications (standalone)).

Pipelines cover NGS quality control, variant calling, coverage analysis, taxonomy, de-novo assembly, RNA-seq, variant calling and more — see the Pipelines catalogue.

Sequana can be used either as a Python library (developers, library users) or via its pipelines and standalones (end users). To join the project, please let us know on github.

Quick start

Install Sequana and run a quality-control pipeline in 2 minutes:

pip install sequana_fastqc
sequana_fastqc --input-directory . --execute

Or use the Python library to read and analyze genomic data:

from sequana import FastA, SequanaCoverage
fasta = FastA("genome.fasta")
cov = SequanaCoverage("coverage.bed")
cov[0].plot_coverage()

Full guides below.

Choosing your entry point

Not sure where to start? This table helps:

What you want to do	Use this
Run a pre-built NGS pipeline (fastqc, variant calling, RNA-seq, etc.)	Pipelines → Tutorial
Use Python to read/analyze sequences, coverage, or variants	Library user guide → API reference
Find a quick helper tool (rename files, filter GFF, count bases)	sequana --help → CLI reference
See working code examples	Gallery or Notebooks

Installation

pip install sequana

Library User Guide

Use Sequana from Python to read, analyze, and visualize genomic data

Tutorial

Step-by-step guides for common workflows and pipelines

Code Examples

Runnable Python examples from the gallery

NGS Pipelines

Browse the Snakemake pipelines catalogue

CLI Reference

The sequana command-line tools (30+ sub-commands)

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Pipeline users

• Installation
  • Quick installation
  • Recommended: virtual environment + pip
  • Bioconda
  • Apptainer / Singularity containers
  • From GitHub (development version)
  • Sequanix (GUI)
  • History
• Pipeline user guide
  • Install a pipeline
  • Initialise the working directory
  • Common CLI options
  • Edit the configuration
  • Run the pipeline
  • Clean up
  • Tips
• Pipelines
  • Quick start
  • Containers
  • Pipeline catalogue
  • Pipeline reference pages
  • Naming convention
• Tutorial
  • The sequana CLI
  • fastqc pipeline
  • Taxonomy (standalone)
  • Variant calling pipeline
  • De-novo assembly
  • RNA-seq
  • Apptainer containers
• Phylogenetic analysis
• Parsing phylogenetic trees (Newick format)
• Multiple sequence alignments
• Combining trees and alignments
• Case examples
• Quality control + variant calling (Measles virus)
• FAQ / Troubleshooting
  • Installation
  • Input data
  • Pipeline runs
  • Library (Python API)
  • PacBio
  • Apptainer / Singularity
  • Open an issue

Library users

• Library user guide
  • Test data
  • Coverage from a BED file
  • FastQ inspection
  • Reading sequence data (FASTA/FASTQ)
  • Annotations (GFF3/GenBank)
  • Variants (VCF)
  • Taxonomy (Kraken)
  • Building HTML report sections from Python
  • Feature counting and differential expression
  • Protein structures (PDB)
  • Where to look next
• Gallery
• Notebooks
  • Notebook map
• CLI reference
• Quick lookup by task
• Full reference
  • sequana

Reference & developers

• Developer guide
  • How to write a new pipeline in Sequana (the new way)
  • Convention to design a rule
  • More information about pipeline design
  • Testing with pytest
  • Module reports
  • Documentation
  • MultiQC
  • Apptainer / Singularity containers
• Applications (standalone)
  • Sequanix: GUI for snakemake workflows
  • sequana_coverage
  • sequana summary (subcommand)
  • sequana mapping (subcommand)
  • sequana_taxonomy
  • fastq related
• Sequanix Tutorial
  • Quick Installation
  • Introduction
  • Sequana pipeline: the quality control example
  • Generic pipeline: a minimalist example with no configuration file
  • Generic pipeline: a minimalist example with a configuration file
  • Dialogs and running analysis locally or on a cluster
  • FAQS
• Wrappers
  • bowtie2/align
  • bowtie2/build
  • add_read_group
  • bam_coverage
  • bcl2fastq
  • blast
  • busco
  • bz2_to_gz
  • canu
  • consensus
  • digital_normalisation
  • dsrc_to_gz
  • falco
  • fastp
  • fastq_stats
  • fastqc
  • feature_counts
  • freebayes
  • freebayes_vcf_filter
  • gz_to_bz2
  • hmmbuild
  • hmmscan
  • index
  • longorfs
  • macs3
  • makeblastdb
  • mark_duplicates
  • minimap2
  • multiqc
  • polypolish
  • predict
  • prokka
  • quast
  • rulegraph
  • sambamba_filter
  • sambamba_markdup
  • samtools_depth
  • sequana_coverage
  • sequana_taxonomy
  • snpeff
  • snpeff_add_locus_in_fasta
  • sort
  • spades
  • trinity
  • trinity_quantify
  • unicycler
• API reference
  • References (IO / file formats)
  • References (genomics: sequences, motifs, proteins, RNA)
  • References (pipeline back-ends)
  • References (utilities and misc)
  • References (enrichment)
  • References (stats)
  • References (Viz)
• Glossary

Indices and tables

• Index

• Module Index

• Search Page