Sequana documentation

Current version: 0.8.3, Jul 30, 2020

Python version

Python 3.6, 3.7.3; most modules are Python2.7 compatible.

Source

See http://github.com/sequana/sequana.

Issues

Please fill a report on github

How to cite

For Sequana in general 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), please cite:

Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer Sequana coverage: detection and characterization of genomic variations using running median and mixture models GigaScience, Volume 7, Issue 12, December 2018, giy110, https://doi.org/10.1093/gigascience/giy110

For Sequanix (GUI for Snakemake pipeline), please cite:

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)

Warning

March 2020

Important notes for developers. Major refactoring for version 0.8 now pushed on master branch. Please use this new branch to create your own branches. If you still want to use the previous version, please checkout the branch master_20_03_2020 instead.

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)

Currently, the available pipelines cover 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, RNA-seq. 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 (not always up-to-date)
  • 1.3. From bioconda
  • 1.4. From Pypi website (released source code)
  • 1.5. From GitHub Source code
  • 1.6. 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. Quality Control pipeline
  • 3.2. Taxonomy (standalone)
  • 3.3. Variant calling pipeline
  • 3.4. De novo
  • 3.5. RNA-seq
  • 3.6. 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: fastq_count
  • 7.7. fastq related: fastq_head
  • 7.8. 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. References
  • 11.1. Adapters
  • 11.2. Assembly related
  • 11.3. BAMTOOLS related
  • 11.4. Coverage (bedtools module)
  • 11.5. CIGAR tools
  • 11.6. Coverage (theoretical)
  • 11.7. Access to online database (e.g. ENA)
  • 11.8. Experimental design
  • 11.9. FASTQ module
  • 11.10. FASTA module
  • 11.11. Sequence module
  • 11.12. Kmer module
  • 11.13. IOTools module
  • 11.14. Taxonomy related (Kraken - Krona)
  • 11.15. Pacbio module
  • 11.16. Phred quality
  • 11.17. Running median
  • 11.18. Snakemake module
  • 11.19. pipeline related module
  • 11.20. Snpeff module
  • 11.21. General tools
  • 11.22. Statistical tools
  • 11.23. Format IO
  • 11.24. VCF module
  • 11.25. Module Reports
  • 11.26. Wrapper to other tools
  • 11.27. Misc
  • 11.28. Visualisation
• 12. FAQS
  • 12.1. Conda related
  • 12.2. What are the dependencies
  • 12.3. Installation issues
  • 12.4. Expected input format
  • 12.5. Sequanix related
  • 12.6. QXcbConnection issue
  • 12.7. Variant Calling pipeline
  • 12.8. Quality Control pipeline
  • 12.9. Singularity
  • 12.10. I got a error "main thread is not in the main loop"
• 13. Changelog
  • 13.1. 0.8.3
  • 13.2. 0.8.2
  • 13.3. 0.8.1
  • 13.4. 0.8.0 (24 March 2020)
  • 13.5. 0.7.2
  • 13.6. 0.7.1
  • 13.7. 0.7.0
  • 13.8. 0.6.X
  • 13.9. Prior 0.5.X
  • 13.10. 2016
• 14. Glossary

Indices and tables

• Index

• Module Index

• Search Page