Sequana documentation

Current version: 0.14.0, Mar 30, 2022

SEQUANA

Python version

3.7, 3.8, 3.9

Documentation

On readthedocs

Issues

On github

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): Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer http://biorxiv.org/content/early/2016/12/08/092478

For Sequanix: Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer. 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)

Sequana 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 tools available in the Sequana project

pipeline or tools	Latest Pypi version	Test passing
https://github.com/sequana/sequana_pipetools
https://github.com/sequana/sequana-wrappers	Not on pypi
https://github.com/sequana/demultiplex
https://github.com/sequana/fastqc
https://github.com/sequana/mapper
https://github.com/sequana/pacbio_qc
https://github.com/sequana/ribofinder
https://github.com/sequana/rnaseq
https://github.com/sequana/variant_calling

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

Contributors

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

Changelog

Version	Description
0.14.0	pinned click>=8.1.0 due to API change (autocomplete) moved tests around to decrease packaging from 16 to 4Mb 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
0.12.7	Fix memory leak in len() of FastA class
0.12.6	remove some rules now in https://github.com/sequana/sequana-wrappers
0.12.5	refactorisation of VCF tools/modules to use vcfpy instead of pyVCF
0.12.4	complete change log before 0.12.4 on readthedocs.org

What is Sequana ?

Sequana is a versatile tool that provides

1. A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).

2. A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable rules (see Rules).

3. Original tools to help in the creation of such pipelines including HTML reports.

4. Standalone applications:

   1. sequana_coverage ease the extraction of genomic regions of interest and genome coverage information

   2. sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated databases to be downloaded.

   3. Sequanix: GUI for snakemake workflows, a GUI for Snakemake workflows (hence Sequana pipelines as well)

The sequana pipelines are various. Since March 2020, they have their own independent life within dedicated github repositories. You may find pipelines for NGS quality control (e.g. adapters removal, phix removal, trimming of bad quality bases), variant calling, characterisation of the genome coverage, taxonomic classification, de-novo assembly, Variant calling, RNA-seq, etc. See the Pipelines section for more information.

Sequana can be used by developers to create new pipelines and by users in the form of applications ready for production. Moreover, Sequanix can be used to set the parameters of pipelines and execute them easily with a graphical user interface.

To join the project, please let us know on github.

Installation

conda install sequana

Examples

Visit our example gallery to use the Python library

NGS pipelines

Learn about available Snakemake pipelines

Standalone applications

Standalone applications including Sequanix (GUI for snakemake) and the sequana_coverage tool.

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User guide and reference

• 1. Installation
  • 1.1. Latest recommended installation method
  • 1.2. Other solutions (overview)
  • 1.3. From bioconda
  • 1.4. From GitHub Source code
  • 1.5. Singularity
• 2. Overview
  • 2.1. Sequana is a Python library
  • 2.2. Sequana provides standalone applications
  • 2.3. Sequana, a pipeline construction facilitator
  • 2.4. Sequana Reports
• 3. Tutorial
  • 3.1. The standalone Sequana
  • 3.2. The fastqc pipeline
  • 3.3. Quality Control pipelines
  • 3.4. Taxonomy (standalone)
  • 3.5. Variant calling pipeline
  • 3.6. De novo
  • 3.7. RNA-seq
  • 3.8. Singularity and Sequanix
• 4. Pipelines
  • 4.1. Quick Start
  • 4.2. Overview
  • 4.3. Installation
  • 4.4. Usage
  • 4.5. List pipelines
• 5. Gallery
• 6. Case Examples
  • 6.1. Effect of the trimming on SNPs detection
• 7. Applications (standalone)
  • 7.1. Sequanix: GUI for snakemake workflows
  • 7.2. sequana_coverage
  • 7.3. sequana_summary
  • 7.4. sequana_mapping
  • 7.5. sequana_taxonomy
  • 7.6. fastq related
  • 7.7. sequana_compressor
• 8. Sequanix Tutorial
  • 8.1. Quick Installation
  • 8.2. Introduction
  • 8.3. Sequana pipeline: the quality control example
  • 8.4. Generic pipeline: a minimalist example with no configuration file
  • 8.5. Generic pipeline: a minimalist example with a configuration file
  • 8.6. Dialogs and running analysis locally or on a cluster
  • 8.7. FAQS
• 9. Developer guide
  • 9.1. How to write a new pipeline in Sequana (the new way)
  • 9.2. Convention to design a rule
  • 9.3. More information about pipeline design
  • 9.4. Testing with pytest
  • 9.5. Module reports
  • 9.6. Documentation
  • 9.7. MultiQC
  • 9.8. Singularity
• 10. Rules
• 11. Wrappers
  • 11.1. fastqc
  • 11.2. rulegraph
  • 11.3. bowtie2
• 12. References
  • 12.1. Assembly related
  • 12.2. BAMTOOLS related
  • 12.3. Coverage (bedtools module)
  • 12.4. CIGAR tools
  • 12.5. Coverage (theoretical)
  • 12.6. Access to online database (e.g. ENA)
  • 12.7. Enrichment
  • 12.8. Experimental design
  • 12.9. FASTQ module
  • 12.10. FASTA module
  • 12.11. Feature counts module
  • 12.12. Sequence module
  • 12.13. Kmer module
  • 12.14. Taxonomy related (Kraken - Krona)
  • 12.15. Pacbio module
  • 12.16. Phred quality
  • 12.17. RiboDesigner
  • 12.18. RNAdiff
  • 12.19. Running median
  • 12.20. Snpeff module
  • 12.21. General tools
  • 12.22. Format IO
  • 12.23. VCF module
  • 12.24. Module Reports
  • 12.25. Wrapper to other tools
  • 12.26. Misc
• 13. References (Viz)
  • 13.1. Visualisation
• 14. References (stats)
  • 14.1. Statistical tools
• 15. FAQS
  • 15.1. Conda related
  • 15.2. What are the dependencies
  • 15.3. Installation issues
  • 15.4. Expected input format
  • 15.5. Sequanix related
  • 15.6. QXcbConnection issue
  • 15.7. Variant Calling pipeline
  • 15.8. Quality Control pipeline
  • 15.9. Singularity
  • 15.10. I got a error "main thread is not in the main loop"
  • 15.11. Installation issue on Mac
• 16. Changelog
  • 16.1. 0.12.3
  • 16.2. 0.12.2
  • 16.3. 0.12.1
  • 16.4. 0.12.0
  • 16.5. 0.11.1
  • 16.6. 0.11
  • 16.7. 0.10.0
  • 16.8. 0.9.8
  • 16.9. 0.9.7
  • 16.10. 0.9.6
  • 16.11. 0.9.5
  • 16.12. 0.9.4
  • 16.13. 0.9.3
  • 16.14. 0.9.2
  • 16.15. 0.9.1
  • 16.16. 0.9.0
  • 16.17. 0.8.6
  • 16.18. 0.8.5
  • 16.19. 0.8.4
  • 16.20. 0.8.3
  • 16.21. 0.8.2
  • 16.22. 0.8.1
  • 16.23. 0.8.0 (24 March 2020)
  • 16.24. 0.7.2
  • 16.25. 0.7.1
  • 16.26. 0.7.0
  • 16.27. 0.6.X
  • 16.28. Prior 0.5.X
  • 16.29. 2016
• 17. Glossary

Indices and tables

• Index

• Module Index

• Search Page